159 results on '"Martin Crespi"'
Search Results
2. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
- Author
-
Camille Fonouni-Farde, Aurélie Christ, Thomas Blein, María Florencia Legascue, Lucía Ferrero, Michaël Moison, Leandro Lucero, Juan Sebastián Ramírez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi, and Federico Ariel
- Subjects
Long noncoding RNA ,DNA methylation ,PRC1 ,Polycomb ,RdDM ,Thermomorphogenesis ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. Conclusions Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
- Published
- 2022
- Full Text
- View/download PDF
3. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
- Author
-
Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wießner-Kroh, Alejandro Paniagua, Martin Crespi, Katherine Denby, Asa ben Hur, Enamul Huq, Michael Jantsch, Artur Jarmolowski, Tino Koester, Sascha Laubinger, Qingshun Quinn Li, Lianfeng Gu, Motoaki Seki, Dorothee Staiger, Ramanjulu Sunkar, Zofia Szweykowska-Kulinska, Shih-Long Tu, Andreas Wachter, Robbie Waugh, Liming Xiong, Xiao-Ning Zhang, Ana Conesa, Anireddy S. N. Reddy, Andrea Barta, Maria Kalyna, and John W. S. Brown
- Subjects
Arabidopsis ,Iso-seq ,Reference transcript dataset ,Splice junction ,Transcription start and end sites ,Alternative splicing ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. Results We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. Conclusions AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
- Published
- 2022
- Full Text
- View/download PDF
4. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation
- Author
-
Haroon Butt, Jeremie Bazin, Sahar Alshareef, Ayman Eid, Moussa Benhamed, Anireddy S. N. Reddy, Martin Crespi, and Magdy M. Mahfouz
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
- Published
- 2021
- Full Text
- View/download PDF
5. Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
- Author
-
Constanza Chialva, Thomas Blein, Martin Crespi, and Diego Lijavetzky
- Subjects
Medicine ,Science - Abstract
Abstract Carrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.
- Published
- 2021
- Full Text
- View/download PDF
6. Wheat chromatin architecture is organized in genome territories and transcription factories
- Author
-
Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Severine Domenichini, Natalia Y. Rodriguez Granados, Soonkap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza-Mianza, Caroline Juery, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, and Moussa Benhamed
- Subjects
Hi-C ,Hi-ChIP ,DNA loops ,Transcription factories ,Genome territories ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. Results We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. Conclusions Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
- Published
- 2020
- Full Text
- View/download PDF
7. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality
- Author
-
Bárbara Hufnagel, André Marques, Alexandre Soriano, Laurence Marquès, Fanchon Divol, Patrick Doumas, Erika Sallet, Davide Mancinotti, Sébastien Carrere, William Marande, Sandrine Arribat, Jean Keller, Cécile Huneau, Thomas Blein, Delphine Aimé, Malika Laguerre, Jemma Taylor, Veit Schubert, Matthew Nelson, Fernando Geu-Flores, Martin Crespi, Karine Gallardo, Pierre-Marc Delaux, Jérôme Salse, Hélène Bergès, Romain Guyot, Jérôme Gouzy, and Benjamin Péret
- Subjects
Science - Abstract
White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
- Published
- 2020
- Full Text
- View/download PDF
8. CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors
- Author
-
Haroon Butt, Ayman Eid, Afaque A. Momin, Jeremie Bazin, Martin Crespi, Stefan T. Arold, and Magdy M. Mahfouz
- Subjects
Directed evolution ,Genome engineering ,Spliceosome ,SF3B complex ,SF3B1 ,Splicing modulators ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Increasing genetic diversity via directed evolution holds great promise to accelerate trait development and crop improvement. We developed a CRISPR/Cas-based directed evolution platform in plants to evolve the rice (Oryza sativa) SF3B1 spliceosomal protein for resistance to splicing inhibitors. SF3B1 mutant variants, termed SF3B1-GEX1A-Resistant (SGR), confer variable levels of resistance to splicing inhibitors. Studies of the structural basis of the splicing inhibitor binding to SGRs corroborate the resistance phenotype. This directed evolution platform can be used to interrogate and evolve the molecular functions of key biomolecules and to engineer crop traits for improved performance and adaptation under climate change conditions.
- Published
- 2019
- Full Text
- View/download PDF
9. The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses
- Author
-
Haroon Butt, Jeremie Bazin, Kasavajhala V. S. K. Prasad, Nourelislam Awad, Martin Crespi, Anireddy S. N. Reddy, and Magdy M. Mahfouz
- Subjects
pre-mRNA splicing ,alternative splicing ,SR proteins ,genome engineering ,abiotic stress ,Cytology ,QH573-671 - Abstract
Abiotic stresses profoundly affect plant growth and development and limit crop productivity. Pre-mRNA splicing is a major form of gene regulation that helps plants cope with various stresses. Serine/arginine (SR)-rich splicing factors play a key role in pre-mRNA splicing to regulate different biological processes under stress conditions. Alternative splicing (AS) of SR transcripts and other transcripts of stress-responsive genes generates multiple splice isoforms that contribute to protein diversity, modulate gene expression, and affect plant stress tolerance. Here, we investigated the function of the plant-specific SR protein RS33 in regulating pre-mRNA splicing and abiotic stress responses in rice. The loss-of-function mutant rs33 showed increased sensitivity to salt and low-temperature stresses. Genome-wide analyses of gene expression and splicing in wild-type and rs33 seedlings subjected to these stresses identified multiple splice isoforms of stress-responsive genes whose AS are regulated by RS33. The number of RS33-regulated genes was much higher under low-temperature stress than under salt stress. Our results suggest that the plant-specific splicing factor RS33 plays a crucial role during plant responses to abiotic stresses.
- Published
- 2022
- Full Text
- View/download PDF
10. Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis.
- Author
-
Jeremie Bazin, Kiruthiga Mariappan, Yunhe Jiang, Thomas Blein, Ronny Voelz, Martin Crespi, and Heribert Hirt
- Subjects
Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1950 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants in the absence of PAMP treatment showed no major splicing changes. However, in contrast to MPK3 and MPK6, MPK4 was found to be a key regulator of PAMP-induced DAS events as the AS of a number of splicing factors and immunity-related protein kinases is affected, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, supporting the notion that PAMP-triggered MPK4 activation mediates regulation of alternative splicing.
- Published
- 2020
- Full Text
- View/download PDF
11. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility
- Author
-
Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz, Heribert Hirt, Cécile Raynaud, and Moussa Benhamed
- Subjects
SWI/SNF ,Chromatin ,Morphogenesis ,Phytochrome Interacting Factor ,G-box ,DNA accessibility ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. Results In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms. Conclusions These results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.
- Published
- 2017
- Full Text
- View/download PDF
12. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations
- Author
-
Camille Fonouni-Farde, Federico Ariel, and Martin Crespi
- Subjects
long noncoding RNA ,post-transcriptional regulation ,target mimicry ,alternative splicing ,protein re-localization ,translation promotion ,Genetics ,QH426-470 - Abstract
The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
- Published
- 2021
- Full Text
- View/download PDF
13. Noncoding RNAs, Emerging Regulators in Root Endosymbioses
- Author
-
Christine Lelandais-Brière, Jérémy Moreau, Caroline Hartmann, and Martin Crespi
- Subjects
Microbiology ,QR1-502 ,Botany ,QK1-989 - Abstract
Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.
- Published
- 2016
- Full Text
- View/download PDF
14. Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
- Author
-
Jérémie Bazin, Natali Romero, Richard Rigo, Celine Charon, Thomas Blein, Federico Ariel, and Martin Crespi
- Subjects
RNA binding proteins ,RNP complexes ,alternative splicing ,immune response ,auxin ,Plant culture ,SB1-1110 - Abstract
Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in Arabidopsis thaliana. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named Alternative Splicing Competitor RNA. Here, we used genome-wide analysis of RNAseq to monitor the NSR global role on multiple tiers of gene expression, including RNA processing and AS. NSRs affect AS of 100s of genes as well as the abundance of lncRNAs particularly in response to auxin. Among them, the FPA floral regulator displayed alternative polyadenylation and differential expression of antisense COOLAIR lncRNAs in nsra/b mutants. This may explains the early flowering phenotype observed in nsra and nsra/b mutants. GO enrichment analysis of affected lines revealed a novel link of NSRs with the immune response pathway. A RIP-seq approach on an NSRa fusion protein in mutant background identified that lncRNAs are privileged direct targets of NSRs in addition to specific AS mRNAs. The interplay of lncRNAs and AS mRNAs in NSR-containing complexes may control the crosstalk between auxin and the immune response pathway.
- Published
- 2018
- Full Text
- View/download PDF
15. LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome.
- Author
-
Alaguraj Veluchamy, Teddy Jégu, Federico Ariel, David Latrasse, Kiruthiga Gayathri Mariappan, Soon-Kap Kim, Martin Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, and Moussa Benhamed
- Subjects
Medicine ,Science - Abstract
Precise expression patterns of genes in time and space are essential for proper development of multicellular organisms. Dynamic chromatin conformation and spatial organization of the genome constitute a major step in this regulation to modulate developmental outputs. Polycomb repressive complexes (PRCs) mediate stable or flexible gene repression in response to internal and environmental cues. In Arabidopsis thaliana, LHP1 co-localizes with H3K27me3 epigenetic marks throughout the genome and interacts with PRC1 and PRC2 members as well as with a long noncoding RNA. Here, we show that LHP1 is responsible for the spreading of H3K27me3 towards the 3' end of the gene body. We also identified a subset of LHP1-activated genes and demonstrated that LHP1 shapes local chromatin topology in order to control transcriptional co-regulation. Our work reveals a general role of LHP1 from local to higher conformation levels of chromatin configuration to determine its accessibility to define gene expression patterns.
- Published
- 2016
- Full Text
- View/download PDF
16. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture.
- Author
-
Teddy Jégu, Séverine Domenichini, Thomas Blein, Federico Ariel, Aurélie Christ, Soon-Kap Kim, Martin Crespi, Stéphanie Boutet-Mercey, Grégory Mouille, Mickaël Bourge, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, and Moussa Benhamed
- Subjects
Medicine ,Science - Abstract
Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.
- Published
- 2015
- Full Text
- View/download PDF
17. The Endosymbiosis-Induced Genes ENOD40 and CCS52a Are Involved in Endoparasitic-Nematode Interactions in Medicago truncatula
- Author
-
Bruno Favery, Arnaud Complainville, Jose Maria Vinardell, Philippe Lecomte, Daniàle Vaubert, Peter Mergaert, Adam Kondorosi, Eva Kondorosi, Martin Crespi, and Pierre Abad
- Subjects
Microbiology ,QR1-502 ,Botany ,QK1-989 - Abstract
Plants associate with a wide range of mutualistic and parasitic biotrophic organisms. Here, we investigated whether beneficial plant symbionts and biotrophic pathogens induce distinct or overlapping regulatory pathways in Medicago truncatula. The symbiosis between Sinorhizobium meliloti and this plant results in the formation of nitrogen-fixing root nodules requiring the activation of specific genes in the host plant. We studied expression patterns of nodule-expressed genes after infection with the root-knot nematode Meloidogyne incognita. Two regulators induced during nodule organogenesis, the early nodulin gene ENOD40 involved in primordium formation and the cell cycle gene CCS52a required for cell differentiation and en-doreduplication, are expressed in galls of the host plant. Expression analysis of promoter-uidA fusions indicates an accumulation of CCS52a transcripts in giant cells undergoing endoreduplication, while ENOD40 expression is localized in surrounding cell layers. Transgenic plants overexpressing ENOD40 show a significantly higher number of galls. In addition, out of the 192 nodule-expressed genes tested, 38 genes were upregulated in nodules at least threefold compared with control roots, but only two genes, nodulin 26 and cyclin D3, were found to be induced in galls. Taken together, these results suggest that certain events, such as endoreduplication, cell-to-cell communication with vascular tissues, or water transport, might be common between giant cell formation and nodule development.
- Published
- 2002
- Full Text
- View/download PDF
18. Temporal and Spatial Order of Events During the Induction of Cortical Cell Divisions in White Clover by Rhizobium leguminosarum bv. trifolii Inoculation or Localized Cytokinin Addition
- Author
-
Ulrike Mathesius, Celine Charon, Barry G. Rolfe, Adam Kondorosi, and Martin Crespi
- Subjects
auxin transport inhibition ,fluorescence ,GH3:gusA ,signal transduction ,Microbiology ,QR1-502 ,Botany ,QK1-989 - Abstract
We examined the timing and location of several early root responses to Rhizobium leguminosarum bv. trifolii infection, compared with a localized addition of cytokinin in white clover, to study the role of cytokinin in early signaling during nodule initiation. Induction of ENOD40 expression by either rhizobia or cytokinin was similar in timing and location and occurred in nodule progenitor cells in the inner cortex. Inoculation of rhizobia in the mature root failed to induce ENOD40 expression and cortical cell divisions (ccd). Nitrate addition at levels repressing nodule formation inhibited ENOD40 induction by rhizobia but not by cytokinin. ENOD40 expression was not induced by auxin, an auxin transport inhibitor, or an ethylene precursor. In contrast to rhizobia, cytokinin addition was not sufficient to induce a modulation of the auxin flow, the induction of specific chalcone synthase genes, and the accumulation of fluorescent compounds associated with nodule initiation. However, cytokinin addition was sufficient for the localized induction of auxin-induced GH3 gene expression and the initiation of ccd. Our results suggest that rhizobia induce cytokinin-mediated events in parallel to changes in auxin-related responses during nodule initiation and support a role of ENOD40 in regulating ccd. We propose a model for the interactions of cytokinin with auxin, ENOD40, flavonoids, and nitrate during nodulation.
- Published
- 2000
- Full Text
- View/download PDF
19. Identification of Novel Putative Regulatory Genes Induced During Alfalfa Nodule Development with a Cold-Plaque Screening Procedure
- Author
-
Florian Frugier, Adam Kondorosi, and Martin Crespi
- Subjects
nodulins ,Microbiology ,QR1-502 ,Botany ,QK1-989 - Abstract
Until now very few plant genes with possible regulatory functions during nodule development have been isolated. We have used a modified cold-plaque screening method to identify new transcripts expressed at low levels that are induced during nodulation. Several clones were isolated and characterized by their mRNA expression patterns during nodule development and in spontaneous nodules. Sequence homology with known genes of other organisms indicated that transcripts corresponded to (i) “basic” genes probably required during the growth of the nodule organ (e.g., structural proteins), (ii) genes related to the metabolic adaptations taking place during nodule morphogenesis and function (e.g., carbonic anhydrase), and (iii) genes containing regulatory motifs and/or homologies (three clones out of the 20 identified). The latter genes encode a zinc-finger-containing protein, a putative protein kinase, and a Wilm's tumor (WT) suppressor homologue, respectively. Expression of the kinase and WT suppressor homologues was induced early in nodulation, although the latter was activated transiently. Accumulation of the Zn-finger gene transcripts was detected at a later stage of development and seems to be regulated in a complex manner. Hence, using a cold-plaque screening procedure, we could identify genes that may play regulatory roles in the signal transduction pathways activated during nodule development.
- Published
- 1998
- Full Text
- View/download PDF
20. Localization of a bacterial group II intron-encoded protein in eukaryotic nuclear splicing-related cell compartments.
- Author
-
Rafael Nisa-Martínez, Philippe Laporte, José Ignacio Jiménez-Zurdo, Florian Frugier, Martin Crespi, and Nicolás Toro
- Subjects
Medicine ,Science - Abstract
Some bacterial group II introns are widely used for genetic engineering in bacteria, because they can be reprogrammed to insert into the desired DNA target sites. There is considerable interest in developing this group II intron gene targeting technology for use in eukaryotes, but nuclear genomes present several obstacles to the use of this approach. The nuclear genomes of eukaryotes do not contain group II introns, but these introns are thought to have been the progenitors of nuclear spliceosomal introns. We investigated the expression and subcellular localization of the bacterial RmInt1 group II intron-encoded protein (IEP) in Arabidopsis thaliana protoplasts. Following the expression of translational fusions of the wild-type protein and several mutant variants with EGFP, the full-length IEP was found exclusively in the nucleolus, whereas the maturase domain alone targeted EGFP to nuclear speckles. The distribution of the bacterial RmInt1 IEP in plant cell protoplasts suggests that the compartmentalization of eukaryotic cells into nucleus and cytoplasm does not prevent group II introns from invading the host genome. Furthermore, the trafficking of the IEP between the nucleolus and the speckles upon maturase inactivation is consistent with the hypothesis that the spliceosomal machinery evolved from group II introns.
- Published
- 2013
- Full Text
- View/download PDF
21. A novel fry1 allele reveals the existence of a mutant phenotype unrelated to 5'->3' exoribonuclease (XRN) activities in Arabidopsis thaliana roots.
- Author
-
Judith Hirsch, Julie Misson, Peter A Crisp, Pascale David, Vincent Bayle, Gonzalo M Estavillo, Hélène Javot, Serge Chiarenza, Allison C Mallory, Alexis Maizel, Marie Declerck, Barry J Pogson, Hervé Vaucheret, Martin Crespi, Thierry Desnos, Marie-Christine Thibaud, Laurent Nussaume, and Elena Marin
- Subjects
Medicine ,Science - Abstract
Mutations in the FRY1/SAL1 Arabidopsis locus are highly pleiotropic, affecting drought tolerance, leaf shape and root growth. FRY1 encodes a nucleotide phosphatase that in vitro has inositol polyphosphate 1-phosphatase and 3',(2'),5'-bisphosphate nucleotide phosphatase activities. It is not clear which activity mediates each of the diverse biological functions of FRY1 in planta.A fry1 mutant was identified in a genetic screen for Arabidopsis mutants deregulated in the expression of Pi High affinity Transporter 1;4 (PHT1;4). Histological analysis revealed that, in roots, FRY1 expression was restricted to the stele and meristems. The fry1 mutant displayed an altered root architecture phenotype and an increased drought tolerance. All of the phenotypes analyzed were complemented with the AHL gene encoding a protein that converts 3'-polyadenosine 5'-phosphate (PAP) into AMP and Pi. PAP is known to inhibit exoribonucleases (XRN) in vitro. Accordingly, an xrn triple mutant with mutations in all three XRNs shared the fry1 drought tolerance and root architecture phenotypes. Interestingly these two traits were also complemented by grafting, revealing that drought tolerance was primarily conferred by the rosette and that the root architecture can be complemented by long-distance regulation derived from leaves. By contrast, PHT1 expression was not altered in xrn mutants or in grafting experiments. Thus, PHT1 up-regulation probably resulted from a local depletion of Pi in the fry1 stele. This hypothesis is supported by the identification of other genes modulated by Pi deficiency in the stele, which are found induced in a fry1 background.Our results indicate that the 3',(2'),5'-bisphosphate nucleotide phosphatase activity of FRY1 is involved in long-distance as well as local regulatory activities in roots. The local up-regulation of PHT1 genes transcription in roots likely results from local depletion of Pi and is independent of the XRNs.
- Published
- 2011
- Full Text
- View/download PDF
22. Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana.
- Author
-
Rebecca Schwab, Alexis Maizel, Virginia Ruiz-Ferrer, Damien Garcia, Martin Bayer, Martin Crespi, Olivier Voinnet, and Robert A Martienssen
- Subjects
Medicine ,Science - Abstract
BackgroundDifferent classes of small RNAs (sRNAs) refine the expression of numerous genes in higher eukaryotes by directing protein partners to complementary nucleic acids, where they mediate gene silencing. Plants encode a unique class of sRNAs, called trans-acting small interfering RNAs (tasiRNAs), which post-transcriptionally regulate protein-coding transcripts, as do microRNAs (miRNAs), and both sRNA classes control development through their targets. TasiRNA biogenesis requires multiple components of the siRNA pathway and also miRNAs. But while 21mer siRNAs originating from transgenes can mediate silencing across several cell layers, miRNA action seems spatially restricted to the producing or closely surrounding cells.Principal findingsWe have previously described the isolation of a genetrap reporter line for TAS3a, the major locus producing AUXIN RESPONS FACTOR (ARF)-regulating tasiRNAs in the Arabidopsis shoot. Its activity is limited to the adaxial (upper) side of leaf primordia, thus spatially isolated from ARF-activities, which are located in the abaxial (lower) side. We show here by in situ hybridization and reporter fusions that the silencing activities of ARF-regulating tasiRNAs are indeed manifested non-cell autonomously to spatially control ARF activities.Conclusions/significanceEndogenous tasiRNAs are thus mediators of a mobile developmental signal and might provide effective gene silencing at a distance beyond the reach of most miRNAs.
- Published
- 2009
- Full Text
- View/download PDF
23. Long non-coding RNAs reveal new regulatory mechanisms controlling gene expression
- Author
-
Martin Crespi
- Subjects
General Medicine - Published
- 2023
24. A conserved <scp>HSF</scp> :miR169: <scp>NF‐YA</scp> loop involved in tomato and Arabidopsis heat stress tolerance
- Author
-
Sombir Rao, Apoorva Gupta, Chandni Bansal, Celine Sorin, Martin Crespi, and Saloni Mathur
- Subjects
Thermotolerance ,Arabidopsis Proteins ,Arabidopsis ,Benzeneacetamides ,Cell Biology ,Plant Science ,Plants, Genetically Modified ,MicroRNAs ,CCAAT-Binding Factor ,Heat Shock Transcription Factors ,Solanum lycopersicum ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetics ,Piperidones ,Plant Proteins ,Transcription Factors - Abstract
Heat stress transcription factors (HSFs) and microRNAs (miRNAs) regulate different stress and developmental networks in plants. Regulatory feedback mechanisms are at the basis of these networks. Here, we report that plants improve their heat stress tolerance through HSF-mediated transcriptional regulation of MIR169 and post-transcriptional regulation of Nuclear Factor-YA (NF-YA) transcription factors. We show that HSFs recognize tomato (Solanum lycopersicum) and Arabidopsis MIR169 promoters using yeast one-hybrid/chromatin immunoprecipitation-quantitative PCR. Silencing tomato HSFs using virus-induced gene silencing (VIGS) reduced Sly-MIR169 levels and enhanced Sly-NF-YA9/A10 target expression. Further, Sly-NF-YA9/A10 VIGS knockdown tomato plants and Arabidopsis plants overexpressing At-MIR169d or At-nf-ya2 mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressing At-NF-YA2 and those expressing a non-cleavable At-NF-YA2 form (miR169d-resistant At-NF-YA2) as well as plants in which At-miR169d regulation is inhibited (miR169d mimic plants) were more sensitive to heat stress, highlighting NF-YA as a negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage of NF-YA by elevated miR169 levels resulted in alleviation of the repression of the heat stress effector HSFA7 in tomato and Arabidopsis, revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of the heat stress response in tomato and Arabidopsis plants.
- Published
- 2022
25. The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA
- Author
-
Thomas Roulé, Aurelie Christ, Nosheen Hussain, Ying Huang, Caroline Hartmann, Moussa Benhamed, Jose Gutierrez-Marcos, Federico Ariel, Martin Crespi, Thomas Blein, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), and BBSRC grant (BB/L016966/1)CNRS (Laboratoire International Associé NOCOSYM)Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation' (MESRI)
- Subjects
marneral ,epigenetics ,Arabidopsis ,seed germination ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,General Medicine ,[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics ,Chromatin ,Triterpenes ,Epigenesis, Genetic ,lncRNA ,chromatin conformation ,LHP1 ,ABA ,Chromobox Protein Homolog 5 ,RNA, Long Noncoding ,enhancer ,cluster ,Abscisic Acid - Abstract
International audience; Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. In this study, we identified the long non-coding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, which controls the local epigenetic activation of its surrounding region in response to abscisic acid (ABA). MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways
- Published
- 2022
26. Beyond transcription: compelling open questions in plant RNA biology
- Author
-
Pablo A Manavella, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, Yiliang Ding, Qianwen Sun, Hunseung Kang, Federico D Ariel, Martin Crespi, Axel J Giudicatti, Qiang Cai, Hailing Jin, Xiaoqi Feng, Yijun Qi, and Craig S Pikaard
- Subjects
Cell Biology ,Plant Science - Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
- Published
- 2022
27. To keep or not to keep: mRNA stability and translatability in root nodule symbiosis
- Author
-
Mauricio Reynoso, María Eugenia Zanetti, Flavio Antonio Blanco, Martin Crespi, Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANPCyTPICT 2016-00582PICT 2017-0581PICT 2016-0333PICT 2017-0069PICT 2017-2272French National Research Agency (ANR)ANR-15-CE20-0002Saclay Plant Sciences-SPS ANR-17-EUR0007CNRS of France (International Associated Laboratories NOCOSYM project), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0301 basic medicine ,Translation ,Small RNA ,Root nodule ,RNA Stability ,Organogenesis ,Plant Science ,Nodulation ,Biology ,Plant Root Nodulation ,01 natural sciences ,03 medical and health sciences ,Symbiosis ,Gene Expression Regulation, Plant ,Nitrogen Fixation ,microRNA ,Gene expression ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Plant Immunity ,Auxin ,Gene ,Plant Proteins ,2. Zero hunger ,Regulation of gene expression ,Regulator ,Fabaceae ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Enod40 ,Rhizobium ,Root Nodules, Plant ,Peptides ,Transcription ,Pathway ,010606 plant biology & botany - Abstract
International audience; Post-transcriptional control of gene expression allows plants to rapidly adapt to changes in their environment. Under low nitrogen conditions, legume plants engage into a symbiosis with soil bacteria that results in the formation of root nodules, where bacteria are allocated and fix atmospheric nitrogen for the plant's benefit. Recent studies highlighted the importance of small RNA-mediated mechanisms in the control of bacterial infection, nodule organogenesis, and the long-distance signaling that balances plant growth and nodulation. Examples of such mechanisms are shoot-to-root mobile microRNAs and small RNA fragments derived from degradation of bacterial transfer RNAs that repress complementary mRNAs in the host plant. Mechanisms of selective mRNA translation also contribute to rapidly modulate the expression of nodulation genes in a cell-specific manner during symbiosis. Here, the most recent advances made on the regulation of mRNA stability and translatability, and the emerging roles of long non-coding RNAs in symbiosis are summarized.
- Published
- 2020
28. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation
- Author
-
Ayman Eid, Martin Crespi, Anireddy S. N. Reddy, Jérémie Bazin, Magdy M. Mahfouz, Sahar Alshareef, Moussa Benhamed, Haroon Butt, Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biology and Program in Cell and Molecular Biology, Colorado State University [Fort Collins] (CSU), King Abdullah University of Science & Technology, and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,Spliceosome ,retention ,Plant molecular biology ,RNA splicing ,intron ,QH301-705.5 ,[SDV]Life Sciences [q-bio] ,Mutant ,Medicine (miscellaneous) ,Biology ,insights ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,target ,03 medical and health sciences ,Gene Expression Regulation, Plant ,snRNP ,Abiotic Stress Responses ,Biology (General) ,Gene ,Plant Proteins ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,molecular Architecture ,tolerance ,lsm2-8 Complex ,fungi ,Wild type ,Intron ,RNA-Binding Proteins ,food and beverages ,Oryza ,Directed evolution ,proteins ,Cell biology ,networks ,Spliceosomes ,RNA Splicing Factors ,General Agricultural and Biological Sciences ,010606 plant biology & botany - Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1 GEX1A RESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants., Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
- Published
- 2021
29. Sequence-unrelated long noncoding RNAs converged to modulate the activity of conserved epigenetic machineries across kingdoms
- Author
-
Juan S. Ramirez-Prado, Leandro Quadrana, Maria Florencia Legascue, Martin Crespi, Daniel Gonzalez, David Latrasse, Aurélie Christ, Camille Fonouni-Farde, Moussa Benhamed, Thomas Blein, Federico Ariel, Lucia Ferrero, Michaël Moison, Leandro Exequiel Lucero, Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Universidad Nacional del Litoral [Santa Fe] (UNL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Blein, Thomas, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
- Subjects
0106 biological sciences ,Genetics ,0303 health sciences ,biology ,Regulator ,Methylation ,biology.organism_classification ,01 natural sciences ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,medicine.anatomical_structure ,Transcription (biology) ,Arabidopsis ,[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics ,DNA methylation ,Ring finger ,medicine ,Epigenetics ,Gene ,030304 developmental biology ,010606 plant biology & botany - Abstract
SUMMARYRNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNAAUXIN-REGULATED PROMOTER LOOP(APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Here, we showed that in addition to the PRC1-component LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1),APOLOinteracts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). TheAPOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis geneYUCCA2by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrated that the lncRNAUHRF1 Protein Associated Transcript(UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology betweenUPATandAPOLO. In addition, we showed that increased levels ofAPOLOorUPAThamper VIM1 and LHP1 binding toYUCCA2promoter. Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation, and reveal that evolutionary unrelated lncRNAs may exert similar functions across kingdoms.
- Published
- 2021
30. A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
- Author
-
Robbie Waugh, Artur Jarmolowski, Qingshun Quinn Li, Sarah Elizabeth Harvey, Cristiane Paula Gomes Calixto, Sascha Laubinger, Dorothee Staiger, Xiao-Ning Zhang, Yamile Marquez, Lianfeng Gu, Anireddy S. N. Reddy, Wenbin Guo, Runxuan Zhang, Gao Yubang, Martin Crespi, Andrea Barta, Motoaki Seki, Asa ben Hur, Theresa Wiebner-Kroh, John W. S. Brown, Liming Xiong, Juan Carlos Entizne, Maho Tanaka, Akihiro Matsui, Max Coulter, Michael F. Jantsch, Richard Kuo, Zofia Szweykowska-Kulinska, Stefan Riegler, Linda Milne, Katherine J. Denby, Enamul Huq, Ramanjulu Sunkar, Shih-Long Tu, Maria Kalyna, Tino Koester, and Andreas Wachter
- Subjects
Gene expression profiling ,Transcriptome ,Polyadenylation ,Arabidopsis ,Alternative splicing ,Arabidopsis thaliana ,splice ,Computational biology ,Biology ,biology.organism_classification ,Gene - Abstract
BackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis.ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage.ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.
- Published
- 2021
31. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
- Author
-
Camille Fonouni-Farde, Aurélie Christ, Thomas Blein, María Florencia Legascue, Lucía Ferrero, Michaël Moison, Leandro Lucero, Juan Sebastián Ramírez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi, Federico Ariel, Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Agencia Nacional de Promoción Científica y Tecnológica (PICT), Universidad Nacional del Litoral Fima Leloir Award (Argentina) International Associated Lab NOCOSYM (CNRS‑CONICET), the Centre National de la Recherche Scientifique (MOMENTUM program), ANR-17-EUR-0007
- Subjects
Ubiquitin-Protein Ligases ,Arabidopsis ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Histones ,LHP1 ,YUCCA2 ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Humans ,Auxin ,RdDM ,UHRF1 ,Indoleacetic Acids ,Arabidopsis Proteins ,DNA ,DNA Methylation ,Plants ,PRC1 ,UPAT ,Polycomb ,CCAAT-Enhancer-Binding Proteins ,RNA, Long Noncoding ,VIM1 ,Thermomorphogenesis ,R‑loop ,APOLO ,Long noncoding RNA - Abstract
Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. Conclusions Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
- Published
- 2021
32. Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Author
-
Jing An, Javier Antunez-Sanchez, Natalia Y. Rodriguez-Granados, Martin Crespi, David Latrasse, Ying Huang, Juan Sebastian Ramirez-Prado, Magdy M. Mahfouz, Federico Ariel, Lorenzo Concia, Moussa Benhamed, Sanchari Sicar, Deborah Manza-Mianza, Fredy Barneche, Heribert Hirt, Aline V. Probst, José F. Gutierrez-Marcos, Rim Brik-Chaouche, Catherine Bergounioux, Cécile Raynaud, Simon Amiard, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], King Abdullah University of Science and Technology (KAUST), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Universidad Nacional del Litoral [Santa Fe] (UNL), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut Universitaire de France (IUF)China Scholar Council fellowships 201806690005, ANR-19-CE20-0001,3DWheat,Une approche tridimensionnelle de génomique fonctionnelle pour identifier les cibles contrôlant la réponse au stress thermique chez le blé(2019), Raynaud, Cécile, and Une approche tridimensionnelle de génomique fonctionnelle pour identifier les cibles contrôlant la réponse au stress thermique chez le blé - - 3DWheat2019 - ANR-19-CE20-0001 - AAPG2019 - VALID
- Subjects
[SDV]Life Sciences [q-bio] ,macromolecular substances ,Interactome ,HiChIP ,Capture Hi-C ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Transcription (biology) ,Arabidopsis ,[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genetics ,Genetics (clinical) ,ComputingMilieux_MISCELLANEOUS ,Epigenomics ,Chromatin loops ,biology ,biology.organism_classification ,Chromatin ,Cell biology ,Chromatin architecture ,Polycomb ,Histone ,biology.protein ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Chromatin Loop ,Reprogramming - Abstract
In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics, and several 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation, we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 levels led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac, a histone modification associated with active transcription, indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.
- Published
- 2021
33. The root‐knot nematode effector MiEFF18 interacts with the plant core spliceosomal protein SmD1 required for giant cell formation
- Author
-
Hervé Vaucheret, Bruno Favery, Jérémie Bazin, Michaël Quentin, Nhat-My Truong, Nathalie Marteu, Nathalie Bouteiller, Joffrey Mejias, Yongpan Chen, Shinichiro Sawa, Pierre Abad, Martin Crespi, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kumamoto University, China Agricultural University (CAU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRA SPE department, INRA-Syngenta Targetome project, French-Japanese bilateral collaboration programme PHC SAKURA 2016 35891VD, French-Chinese bilateral collaboration program PHC XU GUANGQI 2020 45478PF, French Ministere de lEnseignement Superieur, de la Recherche et de lInnovation (MENRT grant), USTH fellowship, as part of the 911-USTH programme of the Ministry of Education and Training of The Socialist Republic of Vietnam, China Scholarship Council 201806350108, French-Japanese bilateral collaboration programme PHC SAKURA 2019 43006VJ, ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-16-CE12-0032,SPLISIL,Dialogue épissage et extinction de l'ARN durant l'expression génétique(2016), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0301 basic medicine ,Spliceosome ,Arabidopsis thaliana ,Physiology ,[SDV]Life Sciences [q-bio] ,Arabidopsis ,Plant Science ,Giant Cells ,Plant Roots ,01 natural sciences ,Host-Parasite Interactions ,03 medical and health sciences ,alternative splicing ,Solanum lycopersicum ,medicine ,Meloidogyne incognita ,Nicotiana benthamiana ,Animals ,Tylenchoidea ,Plant Diseases ,Plant Proteins ,biology ,Effector ,Alternative splicing ,food and beverages ,Helminth Proteins ,medicine.disease ,biology.organism_classification ,Cell biology ,030104 developmental biology ,effector ,Nematode infection ,Giant cell ,RNA splicing ,Spliceosomes ,nucleus ,010606 plant biology & botany - Abstract
International audience; The root-knot nematode Meloidogyne incognita secretes specific effectors (MiEFF) and induces the redifferentiation of plant root cells into enlarged multinucleate feeding 'giant cells' essential for nematode development. Immunolocalizations revealed the presence of the MiEFF18 protein in the salivary glands of M. incognita juveniles. In planta, MiEFF18 localizes to the nuclei of giant cells demonstrating its secretion during plant-nematode interactions. A yeast two-hybrid approach identified the nuclear ribonucleoprotein SmD1 as a MiEFF18 partner in tomato and Arabidopsis. SmD1 is an essential component of the spliceosome, a complex involved in pre-mRNA splicing and alternative splicing. RNA-seq analyses of Arabidopsis roots ectopically expressing MiEFF18 or partially impaired in SmD1 function (smd1b mutant) revealed the contribution of the effector and its target to alternative splicing and proteome diversity. The comparison with Arabidopsis galls data showed that MiEFF18 modifies the expression of genes important for giant cell ontogenesis, indicating that MiEFF18 modulates SmD1 functions to facilitate giant cell formation. Finally, Arabidopsis smd1b mutants exhibited less susceptibility to M. incognita infection, and the giant cells formed on these mutants displayed developmental defects, suggesting that SmD1 plays an important role in the formation of giant cells and is required for successful nematode infection.
- Published
- 2021
34. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations
- Author
-
Martin Crespi, Camille Fonouni-Farde, Federico Ariel, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Nacional del Litoral [Santa Fe] (UNL), Agencia Nacional de Promoción Científica y Tecnológica (PICT), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-19-CE20-0011,PIOSYM,Comprendre le mode d'action d'un facteur de transcription pionnier pendant le développement des nodosités symbiotiques(2019), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0301 basic medicine ,Ariel ,protein re-localization ,lcsh:QH426-470 ,Computational biology ,Review ,Biology ,01 natural sciences ,Biochemistry ,Genome ,03 medical and health sciences ,C ,Keywords: long noncoding RNA ,alternative splicing ,Gene expression ,Genetics ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Epigenetics ,long noncoding RNA ,Molecular Biology ,Post-transcriptional regulation ,Genome size ,Crespi ,translation promotion ,Regulation of gene expression ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Alternative splicing ,Long non-coding RNA ,target mimicry ,lcsh:Genetics ,030104 developmental biology ,post-translational modification ,F ,Fonouni-Farde ,M. Plant Long Noncoding long noncoding RNA ,010606 plant biology & botany ,post-transcriptional regulation - Abstract
International audience; The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
- Published
- 2021
35. A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance
- Author
-
Martin Crespi, Saloni Mathur, Céline Sorin, Sombir Rao, and Chandni Bansal
- Subjects
biology ,Effector ,Arabidopsis ,Mutant ,Transcriptional regulation ,Gene silencing ,Promoter ,biology.organism_classification ,Transcription factor ,Psychological repression ,Cell biology - Abstract
Regulatory feedbacks are at the basis of different stress and developmental networks in plants. Here, we report that tomato and Arabidopsis plants improve their heat stress tolerance through Heat stress transcription factor (HSF)-mediated transcriptional regulation of MIR169 and post-transcriptional regulation of NF-YA transcription factors. We show that HSFs recognize tomato and Arabidopsis MIR169 promoters using yeast-one-hybrid/ChIP-qPCR. Silencing tomato HSFs using virus-induced-gene-silencing (VIGS) reduce Sly-MIR169 levels and enhance Sly-NF-YA9/A10 target expression. Further, tomato transgenic plants overexpressing Sly-MIR169 and Sly-NF-YA9/A10-VIGS knock-down tomato plants as well as Arabidopsis plants overexpressing At-MIR169d and At-nf-ya2 mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressing At-NF-YA2, or those expressing a non-cleavable At-NF-YA2 form (miR169-resistant At-NF-YA2) as well as plants inhibited for At-miRNA169d regulation (miR169d mimic plants) were more sensitive to heat stress, highlighting NF-YA as negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage of NF-YA by elevated miR169 levels result in alleviating the repression of heat stress effectors HSFA7a/b in tomato and Arabidopsis revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of heat stress response in tomato and Arabidopsis plants.
- Published
- 2021
36. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality
- Author
-
Pierre-Marc Delaux, Romain Guyot, Martin Crespi, Erika Sallet, Malika Laguerre, Fanchon Divol, Sébastien Carrère, Benjamin Péret, Patrick Doumas, Cecile Huneau, Matthew R. Nelson, Jemma Taylor, Alexandre Soriano, Jérôme Salse, Laurence Marquès, Veit Schubert, Fernando Geu-Flores, Davide Mancinotti, Jérôme Gouzy, Sandrine Arribat, Karine Gallardo, André Marques, Thomas Blein, Barbara Hufnagel, William Marande, Delphine Aime, Hélène Bergès, Jean Keller, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), The University of Western Australia (UWA), Centre IRD de Montpellier (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), VILLUM Foundation : 15476, Innovate UK, FAPEAL/CNPq (Brasil), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), European Project: 0637420(2007), University of Copenhagen = Københavns Universitet (UCPH), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens [Kew], and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
- Subjects
0106 biological sciences ,0301 basic medicine ,Repetitive Sequences, Nucleic Acid/genetics ,Plant Roots/genetics ,[SDV]Life Sciences [q-bio] ,Plant genetics ,Gene Dosage ,General Physics and Astronomy ,Sequence assembly ,Alkaloids/chemistry ,Plant Roots ,01 natural sciences ,Genome ,Lupinus ,Soil ,Nutrient ,Gene Duplication ,lcsh:Science ,ComputingMilieux_MISCELLANEOUS ,Plant Proteins ,Plant Proteins/metabolism ,2. Zero hunger ,Multidisciplinary ,Ecotype ,food and beverages ,Transcriptome/genetics ,Polymorphism, Single Nucleotide/genetics ,Seeds ,Genome, Plant ,Agricultural genetics ,Synteny/genetics ,Plant domestication ,Science ,Centromere ,Biology ,Lupinus/genetics ,Polymorphism, Single Nucleotide ,Synteny ,Article ,General Biochemistry, Genetics and Molecular Biology ,Crop ,Evolution, Molecular ,03 medical and health sciences ,Alkaloids ,Seeds/physiology ,Centromere/genetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Domestication ,Repetitive Sequences, Nucleic Acid ,Models, Genetic ,fungi ,Genetic Variation ,Molecular Sequence Annotation ,General Chemistry ,Sequence Analysis, DNA ,15. Life on land ,biology.organism_classification ,Plant Leaves ,030104 developmental biology ,Agronomy ,Genomic Structural Variation ,lcsh:Q ,Plant Leaves/metabolism ,Transcriptome ,010606 plant biology & botany - Abstract
White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield., White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
- Published
- 2020
37. The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA
- Author
-
Martin Crespi, Federico Ariel, Thomas Roulé, Thomas Blein, Caroline Hartmann, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), University of Warwick [Coventry], and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0303 health sciences ,Biology ,biology.organism_classification ,01 natural sciences ,Cell biology ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,03 medical and health sciences ,Prophase ,Arabidopsis ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Chromatin Loop ,Epigenetics ,PRC1 ,Enhancer ,Gene ,Reprogramming ,030304 developmental biology ,010606 plant biology & botany - Abstract
Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. Here we identified the long noncoding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, which controls the local epigenetic activation of its surrounding region in response to ABA. MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel noncoding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.
- Published
- 2020
38. ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
- Author
-
Vladimir Daric, Simon Legendre, Martin Crespi, Eric Lambert, Thomas Roulé, Alejandra Camoirano, Nicolás Gaggion, Federico Ariel, Thomas Blein, Enzo Ferrante, Diego H. Milone, Universidad Nacional del Litoral [Santa Fe] (UNL), Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,Root (linguistics) ,Computer science ,Process (engineering) ,AcademicSubjects/SCI02254 ,3D-printed hardware ,Health Informatics ,Plant Roots ,01 natural sciences ,Convolutional neural network ,03 medical and health sciences ,Artificial Intelligence ,convolutional neural networks ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Segmentation ,Throughput (business) ,image segmentation ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,030304 developmental biology ,root system architecture ,0303 health sciences ,Rhizosphere ,business.industry ,Research ,Deep learning ,Plant root ,Pattern recognition ,04 agricultural and veterinary sciences ,Image segmentation ,temporal phenotyping ,Plants ,Computer Science Applications ,Phenotype ,[INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV] ,040103 agronomy & agriculture ,Systems architecture ,AcademicSubjects/SCI00960 ,0401 agriculture, forestry, and fisheries ,Neural Networks, Computer ,Artificial intelligence ,business ,010606 plant biology & botany - Abstract
Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals. Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.; Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals. Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.
- Published
- 2020
39. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold
- Author
-
Natanael Mansilla, Fernando Ibáñez, Javier Martínez Pacheco, Federico Ariel, Michaël Moison, Leandro Exequiel Lucero, José M. Estevez, Aurélie Christ, Martin Crespi, Camille Fonouni-Farde, Moussa Benhamed, Johan Rodríguez-Melo, Jérémie Bazin, Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Fundación Instituto Leloir and IIBBA-CONICET, Instituto de Investigaciones Agrobiotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANPCyTPICT2016-0132PICT2017-0066PICT2016-0007PICT2016-0289Instituto Milenio iBio-Iniciativa Cientifica Milenio, MINECON, CONICET, National University of Río Cuarto = Universidad Nacional de Río Cuarto (UNRC)-National University of Río Cuarto = Universidad Nacional de Río Cuarto (UNRC), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0301 basic medicine ,Arabidopsis ,Plant Development ,Locus (genetics) ,RHD6 ,Plant Science ,Biology ,Root hair ,01 natural sciences ,Plant Roots ,root hairs ,Ribonucleoprotein complex ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Basic Helix-Loop-Helix Transcription Factors ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Epigenetics ,long noncoding RNAs ,Promoter Regions, Genetic ,Molecular Biology ,Transcription factor ,Cell Proliferation ,WRKY42 ,Indoleacetic Acids ,Arabidopsis Proteins ,Plants, Genetically Modified ,Chromatin ,Cell biology ,Cold Temperature ,030104 developmental biology ,Arabidopsis genome ,RNA, Long Noncoding ,Transcription Factor Gene ,APOLO ,010606 plant biology & botany ,Transcription Factors - Abstract
International audience; Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity, leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4. Furthermore, we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter. WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.
- Published
- 2020
40. Long noncoding RNAs shape transcription in plants
- Author
-
Camille Fonouni-Farde, Martin Crespi, Leandro Exequiel Lucero, Federico Ariel, Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANPCyT Saclay Plant Sciences-SPS ANR-17-EUR-0007Centre National de la Recherche Scientifique (CNRS)Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
- Subjects
0106 biological sciences ,Transcription, Genetic ,RNA polymerase II ,Computational biology ,Review ,Biology ,01 natural sciences ,Biochemistry ,Genome ,Long noncoding RNAs ,03 medical and health sciences ,alternative splicing ,Pol II ,Gene expression ,Genetics ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Epigenetics ,MEDIATOR ,Gene ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,RNA ,High-Throughput Nucleotide Sequencing ,Plants ,PRC2 ,PRC1 ,Chromatin ,Polycomb ,genome topology ,biology.protein ,inverted repeats ,RNA, Long Noncoding ,circRNAs ,transcription ,010606 plant biology & botany ,Biotechnology - Abstract
International audience; The advent of novel high-throughput sequencing techniques has revealed that eukaryotic genomes are massively transcribed although only a small fraction of RNAs exhibits protein-coding capacity. In the last years, long noncoding RNAs (lncRNAs) have emerged as regulators of eukaryotic gene expression in a wide range of molecular mechanisms. Plant lncRNAs can be transcribed by alternative RNA polymerases, acting directly as long transcripts or can be processed into active small RNAs. Several lncRNAs have been recently shown to interact with chromatin, DNA or nuclear proteins to condition the epigenetic environment of target genes or modulate the activity of transcriptional complexes. In this review, we will summarize the recent discoveries about the actions of plant lncRNAs in the regulation of gene expression at the transcriptional level.
- Published
- 2020
41. The lncRNAAPOLOinteracts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold
- Author
-
Michaël Moison, Javier Martínez Pacheco, Leandro Lucero, Camille Fonouni-Farde, Johan Rodríguez-Melo, Natanael Mansilla, Aurélie Christ, Jérémie Bazin, Moussa Benhamed, Fernando Ibañez, Martin Crespi, José M. Estevez, and Federico Ariel
- Subjects
0106 biological sciences ,chemistry.chemical_classification ,0303 health sciences ,Transcriptional activity ,Master regulator ,Locus (genetics) ,Root hair ,Biology ,01 natural sciences ,Cell biology ,Chromatin ,03 medical and health sciences ,chemistry ,Auxin ,Epigenetics ,Transcription factor ,030304 developmental biology ,010606 plant biology & botany - Abstract
Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNAAUXIN REGULATED PROMOTER LOOP(APOLO) directly recognizes multiple independent loci across theArabidopsisgenome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show thatAPOLOrecognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controlsRHD6transcriptional activity leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-likeRSL4. Furthermore, we demonstrate thatAPOLOinteracts with the transcription factor WRKY42 and modulates its binding to theRHD6promoter. WRKY42 is required for the activation ofRHD6by low temperatures andWRKY42deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex involvingAPOLOand WRKY42 forms a regulatory hub which activatesRHD6by shaping its epigenetic environment and integrates signals governing RH growth and development.SUMMARYThe lncRNAAPOLOdirectly regulates the transcription of the root hair-master geneRHD6. In response to cold,APOLOis induced and it decoys the H3K27me3-binding protein LHP1 away fromRHD6. In addition,APOLOmodulates the binding of the transcription factor WRKY42 to theRHD6promoter at low temperatures.
- Published
- 2020
42. Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
- Author
-
Aurélie Christ, Martin Crespi, Thomas Roulé, Caroline Hartmann, Christian Godon, Marc Gabriel, Laetitia Scalisi, Coline Balzergue, Marie-Laure Martin-Magniette, Daniel Gautheret, Tracy François, Thomas Blein, Céline Sorin, Thierry Desnos, Laurent Nussaume, Etienne Delannoy, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Séquence, Structure et Fonction des ARN (SSFA), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR–17–EUR–0007 [Saclay Plant SciencesGraduate School of Research] managed under an Investments for theFuture program [grant no. ANR–11–IDEX–0003–02]) and The KingAbdulla University of Science and Technology (KAUST) Interna-tional Program (grant no. OCRF–2014–CRG4), ANR-12-ADAP-0019,RNAdapt,Les ARN non-codants dans l'adaptation de la croissance racinaire à la carence phosphate(2012), ANR-16-CE12-0032,SPLISIL,Dialogue épissage et extinction de l'ARN durant l'expression génétique(2016), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, and Biologie végétale et microbiologie environnementale - UMR7265 (BVME)
- Subjects
0106 biological sciences ,Physiology ,[SDV]Life Sciences [q-bio] ,Arabidopsis ,Plant Science ,Plant Roots ,01 natural sciences ,Genome ,Phosphates ,Transcriptome ,Gene Expression Regulation, Plant ,Stress, Physiological ,Gene expression ,Genetics ,Arabidopsis thaliana ,Gene ,ComputingMilieux_MISCELLANEOUS ,Research Articles ,Ecotype ,2. Zero hunger ,biology ,Genetic Variation ,15. Life on land ,biology.organism_classification ,Adaptation, Physiological ,RNA, Long Noncoding ,Adaptation ,010606 plant biology & botany - Abstract
International audience; Thousands of lncRNAs with ecotype-specific expression, including two that likely regulate primary root growth, are potentially linked to the evolution of regulatory mechanisms among ecotypes.Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsbergerectaof Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.
- Published
- 2020
43. The Arabidopsis lnc RNA ASCO modulates the transcriptome through interaction with splicing factors
- Author
-
Martin Crespi, Jérémie Bazin, Aurélie Christ, Stéphanie Huguet, Michaël Moison, Leandro Exequiel Lucero, Celine Charon, Moussa Benhamed, Natali Romero-Barrios, Federico Ariel, Thomas Blein, Richard Rigo, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), NPCyT (PICT2016-0289and -0007, Argentina), CNRS (Laboratoire International Associé NOCOSYM), the'Laboratoire d’Excellence (LABEX)' Saclay Plant Sciences (SPS, ANR-10-LABX-40), the Ministère Français de l’Enseignement Supérieur et de la Recherche (RR), and the ANR grants (ANR-15-CE20-0002-01 EPISYM and ANR16-CE20-0003-04 SPLISIL), the EPIMMUNITY International project between IPS2, France and KAUST University, Saudi Arabia., ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-15-CE20-0002,EPISYM,Régulations épigénétiques dans le développement de nodules symbiotiques racinaires chez les légumineuses(2015), ANPCyTPICT 2016-0289-0007CNRS (Laboratoire International Associe NOCOSYM) 'Laboratoire d'Excellence (LABEX)' Saclay Plant Sciences (SPS) ANR-10-LABX-40Ministere Francais de l'Enseignement Superieur et de la Recherche French National Research Agency (ANR)ANR-15-CE20-0002-01 EPISYMANR 16-CE20-0003-04 SPLISILIPS2, France KAUST University, Saudi Arabia LabEx Saclay Plant Sciences-SPS ANR-10-LABX-0040-SPS, and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
SmD1b ,Spliceosome ,FLAGELLIN ,Arabidopsis ,CORE SPLICING FACTORS ,Computational biology ,Biology ,core splicing factors ,Biochemistry ,flagellin ,Transcriptome ,purl.org/becyt/ford/1 [https] ,03 medical and health sciences ,SMD1B ,0302 clinical medicine ,PRP8A ,Genetics ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,long noncoding RNA ,purl.org/becyt/ford/1.6 [https] ,Molecular Biology ,Gene ,030304 developmental biology ,Ribonucleoprotein ,2. Zero hunger ,0303 health sciences ,Arabidopsis Proteins ,Alternative splicing ,LONG NONCODING RNA ,Articles ,biology.organism_classification ,Long non-coding RNA ,Alternative Splicing ,PRP8a ,RNA splicing ,RNA, Long Noncoding ,RNA Splicing Factors ,030217 neurology & neurosurgery - Abstract
Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpression of ASCO at the genome-wide level and find a large number of deregulated and differentially spliced genes related to flagellin responses and biotic stress. In agreement, ASCO-silenced plants are more sensitive to flagellin. However, only a minor subset of deregulated genes overlaps with the AS defects of the nsra/b double mutant, suggesting an alternative way of action for ASCO. Using biotin-labeled oligonucleotides for RNA-mediated ribonucleoprotein purification, we show that ASCO binds to the highly conserved spliceosome component PRP8a. ASCO overaccumulation impairs the recognition of specific flagellin-related transcripts by PRP8a. We further show that ASCO also binds to another spliceosome component, SmD1b, indicating that it interacts with multiple splicing factors. Hence, lncRNAs may integrate a dynamic network including spliceosome core proteins, to modulate transcriptome reprogramming in eukaryotes. Fil: Rigo, Richard. Centre National de la Recherche Scientifique; Francia Fil: Bazin, Jérémie. Centre National de la Recherche Scientifique; Francia Fil: Romero Barrios, Natali. Centre National de la Recherche Scientifique; Francia Fil: Moison, Michael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Lucero, Leandro Exequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Christ, Aurelie. Centre National de la Recherche Scientifique; Francia Fil: Benhamed, Moussa. Centre National de la Recherche Scientifique; Francia Fil: Blein, Thomas. Centre National de la Recherche Scientifique; Francia Fil: Huguet, Stephanie. Centre National de la Recherche Scientifique; Francia Fil: Charon, Celine. Centre National de la Recherche Scientifique; Francia Fil: Crespi, Martin. Centre National de la Recherche Scientifique; Francia Fil: Ariel, Federico Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
- Published
- 2020
44. Evolution of the Small Family of Alternative Splicing Modulators Nuclear Speckle RNA-Binding Proteins in Plants
- Author
-
Federico Ariel, Leandro Exequiel Lucero, Fernando Ibáñez, Martin Crespi, Johan Stiben Rodriguez Melo, Jérémie Bazin, Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Investigaciones Agrobiotecnológicas, CONICET, National University of Río Cuarto = Universidad Nacional de Río Cuarto (UNRC)-National University of Río Cuarto = Universidad Nacional de Río Cuarto (UNRC), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)
- Subjects
0106 biological sciences ,0301 basic medicine ,Cytoplasm ,legumes ,RNA-binding protein ,Plant Roots ,01 natural sciences ,Gene Expression Regulation, Plant ,Arabidopsis thaliana ,ALTERNATIVE SPLICING ,Lateral root formation ,Phylogeny ,Genetics (clinical) ,Plant Proteins ,2. Zero hunger ,lncRNA ENOD40 ,education.field_of_study ,biology ,purl.org/becyt/ford/4.4 [https] ,RNA-Binding Proteins ,food and beverages ,nuclear speckle RNA-binding proteins ,Medicago truncatula ,Cell biology ,LEGUMES ,RNA, Long Noncoding ,NUCLEAR SPECKLE RNA-BINDING PROTEINS ,lcsh:QH426-470 ,Lotus japonicus ,Population ,Article ,Evolution, Molecular ,03 medical and health sciences ,alternative splicing ,symbiotic nodule development ,evolution ,Genetics ,Symbiosis ,education ,Cell Nucleus ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,RBP1 ,Alternative splicing ,fungi ,ENOD40 ,LNCRNA ENOD40 ,biology.organism_classification ,EVOLUTION ,lcsh:Genetics ,030104 developmental biology ,lncrna enod40 ,Lotus ,Embryophyta ,purl.org/becyt/ford/4 [https] ,SYMBIOTIC NODULE DEVELOPMENT ,010606 plant biology & botany - Abstract
RNA-Binding Protein 1 (RBP1) was first identified as a protein partner of the long noncoding RNA (lncRNA) ENOD40 in Medicago truncatula, involved in symbiotic nodule development. RBP1 is localized in nuclear speckles and can be relocalized to the cytoplasm by the interaction with ENOD40. The two closest homologs to RBP1 in Arabidopsis thaliana were called Nuclear Speckle RNA-binding proteins (NSRs) and characterized as alternative splicing modulators of specific mRNAs. They can recognize in vivo the lncRNA ALTERNATIVE SPLICING COMPETITOR (ASCO) among other lncRNAs, regulating lateral root formation. Here, we performed a phylogenetic analysis of NSR/RBP proteins tracking the roots of the family to the Embryophytes. Strikingly, eudicots faced a reductive trend of NSR/RBP proteins in comparison with other groups of flowering plants. In Medicago truncatula and Lotus japonicus, their expression profile during nodulation and in specific regions of the symbiotic nodule was compared to that of the lncRNA ENOD40, as well as to changes in alternative splicing. This hinted at distinct and specific roles of each member during nodulation, likely modulating the population of alternatively spliced transcripts. Our results establish the basis to guide future exploration of NSR/RBP function in alternative splicing regulation in different developmental contexts along the plant lineage. Fil: Lucero, Leandro Exequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Bazin, Jeremie. Université Paris-sud; Francia. Centre National de la Recherche Scientifique; Francia. Institut National de la Recherche Agronomique; Francia Fil: Rodriguez Melo, Johan Stiben. Universidad Nacional de Rio Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones Agrobiotecnológicas - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Agrobiotecnológicas; Argentina Fil: Ibañez, Fernando Julio. Universidad Nacional de Rio Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones Agrobiotecnológicas - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Agrobiotecnológicas; Argentina Fil: Crespi, Leandro Martín. Centre National de la Recherche Scientifique; Francia. Institut National de la Recherche Agronomique; Francia. Université Paris-sud; Francia Fil: Ariel, Federico Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
- Published
- 2020
45. Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
- Author
-
Thomas Blein, Heribert Hirt, Martin Crespi, Kiruthiga Mariappan, Ronny Voelz, Jérémie Bazin, Yunhe Jiang, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
- Subjects
Arabidopsis ,Gene Expression ,Biochemistry ,Cell Signaling ,Gene Expression Regulation, Plant ,Gene expression ,Plant Immunity ,Biology (General) ,Post-Translational Modification ,Phosphorylation ,Regulation of gene expression ,0303 health sciences ,Protein Kinase Signaling Cascade ,030302 biochemistry & molecular biology ,Eukaryota ,Genomics ,Plants ,Signaling Cascades ,Cell biology ,Enzymes ,Nucleic acids ,Experimental Organism Systems ,Mitogen-activated protein kinase ,RNA splicing ,Mitogen-Activated Protein Kinases ,Research Article ,Signal Transduction ,QH301-705.5 ,Arabidopsis Thaliana ,Immunology ,Brassica ,Biology ,Research and Analysis Methods ,Genome Complexity ,Microbiology ,03 medical and health sciences ,Model Organisms ,Stress, Physiological ,Plant and Algal Models ,Virology ,Genetics ,Gene Regulation ,Molecular Biology ,Gene ,030304 developmental biology ,Arabidopsis Proteins ,Alternative splicing ,Pathogen-Associated Molecular Pattern Molecules ,Intron ,Organisms ,Biology and Life Sciences ,Proteins ,Computational Biology ,Cell Biology ,RC581-607 ,biology.organism_classification ,Introns ,[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy ,Alternative Splicing ,RNA processing ,biology.protein ,Enzymology ,Animal Studies ,RNA ,Parasitology ,Immunologic diseases. Allergy ,Protein Kinases ,Flagellin - Abstract
Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1950 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants in the absence of PAMP treatment showed no major splicing changes. However, in contrast to MPK3 and MPK6, MPK4 was found to be a key regulator of PAMP-induced DAS events as the AS of a number of splicing factors and immunity-related protein kinases is affected, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, supporting the notion that PAMP-triggered MPK4 activation mediates regulation of alternative splicing., Author summary Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied PAMP-induced alternative splicing in Arabidopsis and identified several hundred differentially alternatively spliced (DAS) genes. Importantly, of these PAMP-induced DAS genes, only 18% overlap with the set of PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of MAPK mutants identified MPK4 as a key regulator of PAMP-induced DAS events. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, showing that PAMP-triggered MPK4 activation mediates regulation of alternative splicing.
- Published
- 2019
46. Thermopriming triggers splicing memory in Arabidopsis
- Author
-
Yong H. Woo, Ge Gao, Natalia Serrano, Anireddy S. N. Reddy, Martin Crespi, Magdy M. Mahfouz, Morad M. Mokhtar, Moussa Benhamed, Alaguraj Veluchamy, Mohamed A. M. Atia, Christoph A Gehring, Jérémie Bazin, Yu Ling, cgcad, Thss, Tsinghua University [Beijing] (THU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Tsinghua University [Beijing], and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,0301 basic medicine ,Hot Temperature ,Arabidopsis thaliana ,Physiology ,RNA Splicing ,[SDV]Life Sciences [q-bio] ,heat-stress priming ,Arabidopsis ,Plant Science ,Biology ,heat responses ,eXtra Botany ,intron retention ,01 natural sciences ,heat stress ,alternative splicing ,03 medical and health sciences ,Gene Expression Regulation, Plant ,heat-stress memory ,Gene expression ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Adaptation ,Heat shock ,stress memory ,ComputingMilieux_MISCELLANEOUS ,2. Zero hunger ,Regulation of gene expression ,heat priming ,fungi ,Alternative splicing ,food and beverages ,stress response ,biology.organism_classification ,Research Papers ,Cell biology ,030104 developmental biology ,Plant—Environment Interactions ,RNA splicing ,Acquired tolerance ,Transcriptome ,Insight ,Priming (psychology) ,Heat-Shock Response ,010606 plant biology & botany - Abstract
Thermopriming induces genome-wide differential gene expression and alternative splicing patterns, and establishes a ‘splicing memory’ that helps plants to survive subsequent and otherwise lethal heat stress., Abiotic and biotic stresses limit crop productivity. Exposure to a non-lethal stress, referred to as priming, can allow plants to survive subsequent and otherwise lethal conditions; the priming effect persists even after a prolonged stress-free period. However, the molecular mechanisms underlying priming are not fully understood. Here, we investigated the molecular basis of heat-shock memory and the role of priming in Arabidopsis thaliana. Comprehensive analysis of transcriptome-wide changes in gene expression and alternative splicing in primed and non-primed plants revealed that alternative splicing functions as a novel component of heat-shock memory. We show that priming of plants with a non-lethal heat stress results in de-repression of splicing after a second exposure to heat stress. By contrast, non-primed plants showed significant repression of splicing. These observations link ‘splicing memory’ to the ability of plants to survive subsequent and otherwise lethal heat stress. This newly discovered priming-induced splicing memory may represent a general feature of heat-stress responses in plants and other organisms as many of the key components are conserved among eukaryotes. Furthermore, this finding could facilitate the development of novel approaches to improve plant survival under extreme heat stress.
- Published
- 2018
47. Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
- Author
-
Katja Baerenfaller, Martin Crespi, Julia Bailey-Serres, Jérémie Bazin, Brian D. Gregory, Sager J. Gosai, University of Zurich, Bailey-Serres, Julia, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Department of Biology, University of Pennsylvania [Philadelphia], Marie Curie European Economic Community Fellowship [PIOF-GA-2012-327954], National Science Foundation (NSF) [MCB-1021969], Eidgenossische Technische Hochschule, Zurich, NSF [DBI-1429826], National Institutes of Health [S10-OD016290-01A1], University of California (UC), and University of Pennsylvania
- Subjects
0301 basic medicine ,RNA, Untranslated ,phosphate deficiency ,Arabidopsis thaliana ,long noncoding RNA ,ribosome footprint profiling ,small peptides ,Arabidopsis ,Plant Biology ,610 Medicine & health ,Biology ,Plant Roots ,Phosphates ,03 medical and health sciences ,Open Reading Frames ,10183 Swiss Institute of Allergy and Asthma Research ,Gene Expression Regulation, Plant ,Translational regulation ,Protein biosynthesis ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,RNA, Messenger ,Gene ,Genetics ,Messenger RNA ,1000 Multidisciplinary ,Vegetal Biology ,Multidisciplinary ,Gene Expression Profiling ,RNA ,Translation (biology) ,Biological Sciences ,Long non-coding RNA ,Open reading frame ,030104 developmental biology ,PNAS Plus ,Seedlings ,Starvation ,Protein Biosynthesis ,Mutation ,RNA, Long Noncoding ,Transcriptome ,Ribosomes ,Biologie végétale - Abstract
Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs., Proceedings of the National Academy of Sciences of the United States of America, 114 (46), ISSN:0027-8424, ISSN:1091-6490
- Published
- 2017
48. TMV induces RNA decay pathways to modulate gene silencing and disease symptoms
- Author
-
Martin Crespi, Maria Cecilia Rodriguez, Andrea Laura Venturuzzi, Diego Zavallo, Sebastian Asurmendi, Gabriela Conti, INTA, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT) [PICT 2011-938, PICT 2014-1163], INTA [PE 1131022], CONICET, ANPCyT, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,Small interfering RNA ,Tobamovirus del Mosaico del Tabaco ,RNA Stability ,[SDV]Life Sciences [q-bio] ,Plant Science ,RNA decay ,Plant Viruses ,purl.org/becyt/ford/1 [https] ,Gene Expression Regulation, Plant ,Gene expression ,2. Zero hunger ,Genetics ,Exosome Multienzyme Ribonuclease Complex ,Reverse Transcriptase Polymerase Chain Reaction ,Plants, Genetically Modified ,Cell biology ,Antisense RNA ,Tobacco Mosaic Virus ,ARN ,defense ,RNA silencing ,Rna Decay ,RNA, Plant ,RNA Interference ,Signal Transduction ,Gene Expression Regulation, Viral ,RNA-induced silencing complex ,Trans-acting siRNA ,Biology ,PTGS ,Tobacco Mosaic Tobamovirus ,03 medical and health sciences ,Tobacco ,Defense ,exosome ,Gene silencing ,Gene Silencing ,purl.org/becyt/ford/1.6 [https] ,Plant Diseases ,Ptgs ,Virus de las Plantas ,fungi ,RNA ,Cell Biology ,Genética ,Exosome ,Tmv ,Plant Leaves ,TMV ,030104 developmental biology ,Symptoms ,symptoms - Abstract
RNA decay pathways comprise a combination of RNA degradation mechanisms that are implicated in gene expression, development and defense responses in eukaryotes. These mechanisms are known as the RNA Quality Control or RQC pathways. In plants, another important RNA degradation mechanism is the post-transcriptional gene silencing (PTGS) mediated by small RNAs (siRNAs). Notably, the RQC pathway antagonizes PTGS by preventing the entry of dysfunctional mRNAs into the silencing pathway to avoid global degradation of mRNA by siRNAs. Viral transcripts must evade RNA degrading mechanisms, thus viruses encode PTGS suppressor proteins to counteract viral RNA silencing. Here, we demonstrate that tobacco plants infected with TMV and transgenic lines expressing TMV MP and CP (coat protein) proteins (which are not linked to the suppression of silencing) display increased transcriptional levels of RNA decay genes. These plants also showed accumulation of cytoplasmic RNA granules with altered structure, increased rates of RNA decay for transgenes and defective transgene PTGS amplification. Furthermore, knockdown of RRP41 or RRP43 RNA exosome components led to lower levels of TMV accumulation with milder symptoms after infection, several developmental defects and miRNA deregulation. Thus, we propose that TMV proteins induce RNA decay pathways (in particular exosome components) to impair antiviral PTGS and this defensive mechanism would constitute an additional counter-defense strategy that lead to disease symptoms. Fil: Conti, Gabriela. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Venturuzzi, Andrea Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Rodriguez, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Crespi, Martin. Université Paris Sud; Francia. Centre National de la Recherche Scientifique; Francia Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
- Published
- 2016
49. Alternative Splicing in the Regulation of Plant–Microbe Interactions
- Author
-
Martin Crespi, Richard Rigo, J�r�mie Bazin, C�line Charon, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and ANR-16-CE12-0032,SPLISIL,Dialogue épissage et extinction de l'ARN durant l'expression génétique(2016)
- Subjects
0106 biological sciences ,Physiology ,Plant Science ,Computational biology ,Biology ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Stress, Physiological ,Mycorrhizae ,Transcriptional regulation ,Protein Isoforms ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Gene ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Mechanism (biology) ,fungi ,Alternative splicing ,food and beverages ,Cell Biology ,General Medicine ,Plants ,Nonsense Mediated mRNA Decay ,Alternative Splicing ,Host-Pathogen Interactions ,Proteome ,Adaptation ,Rhizobium ,Signal Transduction ,010606 plant biology & botany - Abstract
As sessile organisms, plants are continuously exposed to a wide range of biotic interactions. While some biotic interactions are beneficial or even essential for the plant (e.g. rhizobia and mycorrhiza), others such as pathogens are detrimental and require fast adaptation. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of genes they express. In the past few years, high-throughput transcriptome sequencing have revealed that, in addition to transcriptional control of gene expression, post-transcriptional processes, notably alternative splicing (AS), emerged as a key mechanism for gene regulation during plant adaptation to the environment. AS not only can increase proteome diversity by generating multiple transcripts from a single gene but also can reduce gene expression by yielding isoforms degraded by mechanisms such as nonsense-mediated mRNA decay. In this review, we will summarize recent discoveries detailing the contribution of AS to the regulation of plant–microbe interactions, with an emphasis on the modulation of immunity receptor function and other components of the signaling pathways that deal with pathogen responses. We will also discuss emerging evidences that AS could contribute to dynamic reprogramming of the plant transcriptome during beneficial interactions, such as the legume–symbiotic interaction.
- Published
- 2019
50. Wheat chromatin architecture is organized in genome territories and transcription factories
- Author
-
Susan Duncan, Soon-Kap Kim, Chang Liu, Anthony Hall, Thomas Blein, Ying Huang, Alaguraj Veluchamy, Magali Perez, Azahara Martin-Ramirez, Deborah Manza-Mianza, Martin Crespi, Abdelhafid Bendahmane, Catherine Bergounioux, Etienne Paux, Cécile Raynaud, Graham Moore, Moussa Benhamed, Clement Pichot, Heribert Hirt, Natalia Y. Rodriguez Granados, Lorenzo Concia, David Latrasse, Caroline Juery, Magdy M. Mahfouz, Juan S. Ramirez-Prado, Séverine Domenichini, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Earlham Institute [Norwich], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR-19-CE20-0001,3DWheat,Une approche tridimensionnelle de génomique fonctionnelle pour identifier les cibles contrôlant la réponse au stress thermique chez le blé(2019), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,Transcription factories ,lcsh:QH426-470 ,Euchromatin ,Transcription, Genetic ,RNA polymerase II ,01 natural sciences ,Genome ,DNA loops ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Polyploidy ,03 medical and health sciences ,Hi-C ,Constitutive heterochromatin ,lcsh:QH301-705.5 ,Gene ,Triticum ,Genome territories ,030304 developmental biology ,0303 health sciences ,biology ,Research ,Chromosome ,Chromatin ,Histone Code ,lcsh:Genetics ,lcsh:Biology (General) ,Evolutionary biology ,Hi-ChIP ,biology.protein ,RNA Polymerase II ,Genome, Plant ,010606 plant biology & botany - Abstract
Background Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. Results We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. Conclusions Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
- Published
- 2019
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.