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18. Additional file 3 of The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants

Author

Fonouni-Farde, Camille, Christ, Aurélie, Blein, Thomas, Legascue, María Florencia, Ferrero, Lucía, Moison, Michaël, Lucero, Leandro, Ramírez-Prado, Juan Sebastián, Latrasse, David, Gonzalez, Daniel, Benhamed, Moussa, Quadrana, Leandro, Crespi, Martin, and Ariel, Federico

Abstract

Additional file 3. Peer review history.

Published
2022
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19. Additional file 1 of The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants

Author

Fonouni-Farde, Camille, Christ, Aurélie, Blein, Thomas, Legascue, María Florencia, Ferrero, Lucía, Moison, Michaël, Lucero, Leandro, Ramírez-Prado, Juan Sebastián, Latrasse, David, Gonzalez, Daniel, Benhamed, Moussa, Quadrana, Leandro, Crespi, Martin, and Ariel, Federico

Abstract

Additional file 1: Figure S1. GFP-VIM1 localizes at the nucleus. Figure S2. Characterization of Arabidopsis thaliana VIM1 over-expression and vim1 homozygous T-DNA insertion lines. Figure S3. VIM1, VIM2 and VIM3 are differentially regulated in reponse to heat. Figure S4. APOLO and VIM1 regulate hypocotyle elongation in response to heat. Figure S5. Gene categories transcriptionally regulated in thermomorphogenesis. Figure S6. Epigenetic profile of the YUCCA2 locus. Figure S7. de novo DNA methylation and its maintenance regulate thermomorphogenesis. Figure S8. Bimolecular Fluorescence Complementation (BiFC) assay in transiently transformed Nicotiana benthamiana leaves. Figure S9. APOLO and UPAT lncRNAs share mechanisms of interaction with methylcytosine-binding proteins but no sequence similarity [133]. Figure S10. Constitutive expression of the lncRNA UPAT in Arabidopsis seedlings impairs YUCCA2 transcriptional accumulation. Figure S11. CRISPR/Cas9 strategy for APOLO deletion.

Published
2022
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24. Genetic and environmental modulation of natural transposition enhances the adaptive potential of Arabidopsis thaliana

Author

Baduel, Pierre, Leduque, Basile, Gil, José, Loudet, Olivier, Vincent, Colot, Quadrana, Leandro, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), Institut Curie [Paris], Institut Jean-Pierre Bourgin (IJPB), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

How species can adapt to rapid environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leveraged multi-omics sequencing data available for >1,000 wild A. thaliana accessions to determine the contribution of transposable element (TE) mobilization to the creation of new variation. We show that overall, transposition-induced insertion substitutions occur almost at the same rate as SNPs. However, transpositional activity of individual TE families varies greatly between accessions, in association with genetic and environmental factors and we identified in addition important gene-environment interactions. Although the distribution of TE insertions across the genome is ultimately mainly shaped by purifying selection, numerous recent transposition events show signatures of positive selection in relation to local climates. Based on these findings, we generated mathematical models to forecast the impact of global warming on TE mobilization. Our models predict higher transposition activity in central parts of the species' range, which in turn will enhance the generation of potentially adaptive TE-containing alleles and may rescue native A. thaliana populations from extinction.

Published
2021

31. Sequence-unrelated long noncoding RNAs converged to modulate the activity of conserved epigenetic machineries across kingdoms

Author

Fonouni-Farde, Camille, primary, Christ, Aurélie, additional, Blein, Thomas, additional, Ramírez-Prado, Juan Sebastián, additional, Legascue, María Florencia, additional, Latrasse, David, additional, Moison, Michaël, additional, Lucero, Leandro, additional, Ferrero, Lucía, additional, Gonzalez, Daniel, additional, Benhamed, Moussa, additional, Quadrana, Leandro, additional, Crespi, Martin, additional, and Ariel, Federico, additional

Published
2021
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32. Altering PRC2 activity partially suppresses ddm1 mutant phenotypes in Arabidopsis

Author

Rougée, Martin, Quadrana, Leandro, Zervudacki, Jérôme, Colot, Vincent, Navarro, Lionel, Deleris, Angélique, 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), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-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)-École normale supérieure - Paris (ENS Paris), and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, fungi, food and beverages, [SDV.IB]Life Sciences [q-bio]/Bioengineering, macromolecular substances
Abstract

12 13 In plants and mammals, DNA methylation is a hallmark of transposable element (TE) 14 sequences that contributes to their epigenetic silencing. In contrast, histone H3 lysine 27 15 trimethylation (H3K27me3), which is deposited by the Polycomb Repressive Complex 2 16 (PRC2), is a hallmark of repressed genes. Nevertheless, there is a growing body of evidence for 17 a functional interplay between these pathways. In particular, many TE sequences acquire 18 H3K27me3 when they lose DNA methylation and it has been proposed that PRC2 can serve as 19 a backup silencing system for hypomethylated TEs. Here, we describe in the flowering plant 20 Arabidopsis thaliana the gain of H3K27m3 at hundreds of TEs in the mutant ddm1, which is 21 defective in the maintenance of DNA methylation specifically over TE and other repeat 22 sequences. Importantly, we show that this gain depends solely on CURLY LEAF (CLF), which 23 is one of two otherwise partially redundant H3K27 methyltransferases active in vegetative 24 tissues. Finally, our results challenge the notion that PRC2 can be a compensatory silencing 25 system for hypomethylated TEs, as the complete loss of H3K27me3 in ddm1 clf double mutant 26 plants was not associated with further reactivation of TE expression nor with a burst of 27 transposition. Instead, and surprisingly, ddm1 clf plants exhibited less activated TEs, and a 28 chromatin recompaction as well as hypermethylation of linker DNA compared to ddm1. Thus, 29 we have described an unexpected genetic interaction between DNA methylation and Polycomb 30 silencing pathways, where a mutation in PRC2 does not aggravate the molecular phenotypes 31 linked to TE hypomethylation in ddm1 but instead partially suppresses them.

Published
2019

33. Mild drought induces phenotypic and DNA methylation plasticity but no 1 transgenerational effects in Arabidopsis 2 3

Author

Dooren, Tom Van, Bortolini Silveira, Amanda, Gilbault, Elodie, Jiménez-Gómez, José, Martin, Antoine, Bach, Lien, Tisne, Sebastien, Quadrana, Leandro, Loudet, Olivier, Colot, Vincent, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Service d'Anatomie et de Cytologie Pathologiques [Avicenne], Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Avicenne, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Avicenne [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris 13 (UP13)

Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
Published
2019

34. Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato

Author

Burgos, Estanislao, primary, Belen De Luca, Maria, additional, Diouf, Isidore, additional, Haro, Luis A., additional, Albert, Elise, additional, Sauvage, Christopher, additional, Tao, Zhao J., additional, Bermudez, Luisa, additional, Asís, Ramon, additional, Nesi, Adriano N., additional, Matringe, Michel, additional, Bréhélin, Claire, additional, Guiraud, Thomas, additional, Ferrand, Carine, additional, Atienza, Isabelle, additional, Jorly, Joana, additional, Mauxion, Jean P., additional, Baldet, Pierre, additional, Fernie, Alisdair R., additional, Quadrana, Leandro, additional, Rothan, Christophe, additional, Causse, Mathilde, additional, and Carrari, Fernando, additional

Published
2020
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39. Additional file 6: of Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Author

Legrand, Sylvain, Caron, Thibault, Maumus, Florian, Schvartzman, Sol, Quadrana, Leandro, Durand, Eléonore, Gallina, Sophie, Pauwels, Maxime, Mazoyer, Clément, Huyghe, Lucie, Colot, Vincent, Hanikenne, Marc, and Castric, Vincent

Subjects
animal structures, food and beverages
Abstract

Strategy to identify orthology relationships of TE sequences as determined by positional information from the flanking genes. The first step consists in defining the orthology of genes (blue squares) between genomes X and Y using Inparanoid. In our example, A/A’, C/C′ and E/E’ are considered as orthologous pair of genes (represented by blue arrows). The orthology of TEs is defined sequentially for genome X and Y but the process are similar: only TEs between two orthologous genes spaced for at most 70 kb (black squares named a and b in our example) (named “Framed”) and TEs located within genes (black square c) (named “Inserted”) are analysed. TEs which are located at an extremity of a scaffold (d and d’) and TEs located on scaffold without orthologous genes are discarded. The sequence of the TE a and b, which are located between A and C genes of the orthology map are compared using Blastn (thresholds: Evalue ≤1E− 10, an identity ≥80%) to the sequence between the orthologous genes of A and C, i.e. A’ and C′. The TE a presents a blast hit, and a TE annotation overlaps the Blast hit in genome Y. Hence a and a’ are defined as orthologous. No-significant blast hit is retrieved for b, which is defined as non-orthologous. The sequence of the TE c located within the E gene is compared to the sequence of the E’ gene. In our example, we considered that the Blast hit is significant and overlaps a TE annotation in Genome Y. The TE c is defined as orthologous. (PDF 11 kb)

Published
2019
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40. Additional file 4: of Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Author

Legrand, Sylvain, Caron, Thibault, Maumus, Florian, Schvartzman, Sol, Quadrana, Leandro, Durand, Eléonore, Gallina, Sophie, Pauwels, Maxime, Mazoyer, Clément, Huyghe, Lucie, Colot, Vincent, Hanikenne, Marc, and Castric, Vincent

Subjects
food and beverages
Abstract

Identification of factors related to the long-term maintenance of TEs using the comparison of the TE content from A. halleri gemmifera and A. lyrata. A: distribution of nucleotide identity of TEs to the consensus sequence of their TE family, B: superfamily composition, C: TE length, D: frequency of orthologous and non-orthologous TEs within genic sequences, E: frequency of orthologous and non-orthologous TEs within different categories of genic sequences, F: distance to the nearest gene for TEs outside of genes. Statistical significance is indicated using the following code: “***” for p 0.1. (PDF 137 kb)

Published
2019
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42. Additional file 5: of Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Author

Legrand, Sylvain, Caron, Thibault, Maumus, Florian, Schvartzman, Sol, Quadrana, Leandro, ElĂŠonore Durand, Gallina, Sophie, Pauwels, Maxime, ClĂŠment Mazoyer, Huyghe, Lucie, Colot, Vincent, Hanikenne, Marc, and Castric, Vincent

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Hardware_ARITHMETICANDLOGICSTRUCTURES
Abstract

Pipeline used for the deep repeatome annotation. (PDF 30 kb)

Published
2019
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43. Additional file 1: of Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Author

Legrand, Sylvain, Caron, Thibault, Maumus, Florian, Schvartzman, Sol, Quadrana, Leandro, ElĂŠonore Durand, Gallina, Sophie, Pauwels, Maxime, ClĂŠment Mazoyer, Huyghe, Lucie, Colot, Vincent, Hanikenne, Marc, and Castric, Vincent

Abstract

Summary statistics of input sequence data for de novo assembly of the A. halleri genome. (PDF 46 kb)

Published
2019
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44. Additional file 2: of Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Author

Legrand, Sylvain, Caron, Thibault, Maumus, Florian, Schvartzman, Sol, Quadrana, Leandro, ElĂŠonore Durand, Gallina, Sophie, Pauwels, Maxime, ClĂŠment Mazoyer, Huyghe, Lucie, Colot, Vincent, Hanikenne, Marc, and Castric, Vincent

Subjects
food and beverages
Abstract

Distribution of identity of TEs to the consensus sequence of their TE family, separated by superfamily. For each species, superfamilies are sorted according their contribution to the peaks of the most recent population of TEs (using a threshold of 98%). (PDF 91 kb)

Published
2019
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47. Transposition favors the generation of large effect mutations that may facilitate rapid adaption

Author

Quadrana, Leandro, primary, Etcheverry, Mathilde, additional, Gilly, Arthur, additional, Caillieux, Erwann, additional, Madoui, Mohammed-Amin, additional, Guy, Julie, additional, Bortolini Silveira, Amanda, additional, Engelen, Stefan, additional, Baillet, Victoire, additional, Wincker, Patrick, additional, Aury, Jean-Marc, additional, and Colot, Vincent, additional

Published
2019
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48. Transposon accumulation lines uncover histone H2A.Z-driven integration bias towards environmentally responsive genes

Author

Quadrana, Leandro, primary, Etcheverry, Mathilde, additional, Gilly, Arthur, additional, Caillieux, Erwann, additional, Madoui, Mohammed-Amin, additional, Guy, Julie, additional, Silveira, Amanda Bortolini, additional, Engelen, Stefan, additional, Baillet, Victoire, additional, Wincke, Patrick, additional, Aury, Jean-Marc, additional, and Colot, Vincent, additional

Published
2018
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49. Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato.

Author

Burgos, Estanislao, Belen De Luca, Maria, Diouf, Isidore, Haro, Luis A., Albert, Elise, Sauvage, Christopher, Tao, Zhao J., Bermudez, Luisa, Asís, Ramon, Nesi, Adriano N., Matringe, Michel, Bréhélin, Claire, Guiraud, Thomas, Ferrand, Carine, Atienza, Isabelle, Jorly, Joana, Mauxion, Jean P., Baldet, Pierre, Fernie, Alisdair R., and Quadrana, Leandro

Subjects
VITAMIN E, TRANSGENIC plants, NUTRITIONAL value, METABOLISM, GENES, TOMATOES, LEMNA minor
Abstract

Summary: Tocochromanols constitute the different forms of vitamin E (VTE), essential components of the human diet, and display a high membrane protectant activity. By combining interval mapping and genome‐wide association studies (GWAS), we unveiled the genetic determinants of tocochromanol accumulation in tomato (Solanum lycopersicum) fruits. To enhance the nutritional value of this highly consumed vegetable, we dissected the natural intraspecific variability of tocochromanols in tomato fruits and genetically engineered their biosynthetic pathway. These analyses allowed the identification of a total of 25 quantitative trait loci interspersed across the genome pinpointing the chorismate–tyrosine pathway as a regulatory hub controlling the supply of the aromatic head group for tocochromanol biosynthesis. To validate the link between the chorismate–tyrosine pathway and VTE, we engineered tomato plants to bypass the pathway at the arogenate branch point. Transgenic tomatoes showed moderate increments in tocopherols (up to approximately 20%) and a massive accumulation of tocotrienols (up to approximately 3400%). Gene expression analyses of these plants reveal a trade‐off between VTE and natural variation in chorismate metabolism explained by transcriptional reprogramming of specific structural genes of the pathway. By restoring the accumulation of alpha‐tocotrienols (α‐t3) in fruits, the plants produced here are of high pharmacological and nutritional interest. Significance Statement: In this ms, we contribute with a large scale genetic analysis applying multi‐parental advanced generation intercross and genome‐wide association study population mapping, which allowed us to detect a trade‐off between vitamin E accumulation and chorismate metabolism. Moreover, validation experiments with engineered transgenic plants revealed massive accumulation of α‐tocotrienol, a minor form of tocochromanol with higher VTE activity than that recognized to date. By restoring the accumulation of this compound in fruits, the plants produced here are of pharmacological and nutritional interest. [ABSTRACT FROM AUTHOR]

Published
2021
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