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DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, in which modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effector molecules, several of which act as proteasome inhibitors. Here, we investigated the effect of proteasome inhibition by the bacterial virulence factor syringolin A (SylA) on genome-wide DNA methylation. We show that SylA treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH differentially methylated regions (DMRs) that are enriched in the proximity of transcriptional start sites. SylA treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway, namely AGO3, AGO9, and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of an epi-genomic arms race against pathogens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.

While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.

The ability to decipher the three-dimensional chromosome folding in many eukaryotes is a major asset in molecular biology. It is not only required to study the biological relevance of chromosome folding in cellular processes but also for the de novo assembly of genomes of nonmodel species. With lowering DNA sequencing costs, the latter has recently become interesting to many scientists, ranging from molecular biologists that aim to establish new model organisms, to evolutionary biologists and ecologists, interested in genome evolution and diversity. Hi-C is regarded as the method of choice to characterize three-dimensional genome folding and, thus, also has been integrated as a standard method in assembly pipelines. However, Hi-C is a demanding molecular biology technique, and its application can be considerably challenged by the tissue used. Hi-C relies on efficient and pure nuclei isolation, which is, especially in many plant species, inhibited by the tough nature of plant tissues and cell walls. The Hi-C protocol presented here has been optimized for such tissues and has been shown to generate Hi-C samples of sufficient quality in various plant and animal tissues.

Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.

Linker histones play a pivotal role in shaping chromatin architecture, notably through their globular H1 (GH1) domain that contacts the nucleosome and linker DNA. Yet, the interplay of H1 with chromatin factors along the epigenome landscape is poorly understood. Here, we report that Arabidopsis H1 favors chromatin compaction and H3K27me3 marking on a majority of Polycomb-targeted protein-coding genes while preventing H3K27me3 accumulation on telomeres and pericentromeric interstitial telomeric repeats (ITRs). These contrasting effects of H1 on H3K27me3 enrichment are associated with long-distance effects on the 3D organization of telomeres and ITRs. Mechanistically, H1 prevents ITRs from being invaded by Telomere Repeat Binding 1 (TRB1), a GH1-containing telomere component with an extra-telomeric function in targeting Polycomb to genes bearing telomeric motifs. We propose that reciprocal DNA binding of H1 and TRB1 to clustered telobox motifs prevents H3K27me3 accumulation on large chromosomal blocks, conferring a sequence-specific role to H1 in epigenome homeostasis.

Background The three-dimensional (3D) organization of chromosomes is linked to epigenetic regulation and transcriptional activity. However, only few functional features of 3D chromatin architecture have been described to date. The KNOT is a 3D chromatin structure in Arabidopsis, comprising 10 interacting genomic regions termed KNOT ENGAGED ELEMENTs (KEEs). KEEs are enriched in transposable elements and associated small RNAs, suggesting a function in transposon biology. Results Here, we report the KNOT’s involvement in regulating invasive DNA elements. Transgenes can specifically interact with the KNOT, leading to perturbations of 3D nuclear organization, which correlates with the transgene’s expression: high KNOT interaction frequencies are associated with transgene silencing. KNOT-linked silencing (KLS) cannot readily be connected to canonical silencing mechanisms, such as RNA-directed DNA methylation and post-transcriptional gene silencing, as both cytosine methylation and small RNA abundance do not correlate with KLS. Furthermore, KLS exhibits paramutation-like behavior, as silenced transgenes can lead to the silencing of active transgenes in trans. Conclusion Transgene silencing can be connected to a specific feature of Arabidopsis 3D nuclear organization, namely the KNOT. KLS likely acts either independent of or prior to canonical silencing mechanisms, such that its characterization not only contributes to our understanding of chromosome folding but also provides valuable insights into how genomes are defended against invasive DNA elements.

BACKGROUND: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. RESULTS: We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation-complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. CONCLUSIONS: H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions.

Background Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. Results We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. Conclusions The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

Multiples lines of evidence indicate that spatial 3D organisation nuclear DNA is critical in adapting to different environmental conditions and the Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH) network aims to decipher how nuclear architecture, chromatin organisation and gene expression are connected and modified in response to internal and external cues.

Multiples lines of evidence indicate that spatial 3D organisation nuclear DNA is critical in adapting to different environmental conditions and the Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH) network aims to decipher how nuclear architecture, chromatin organisation and gene expression are connected and modified in response to internal and external cues.

Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues. This method is quantitative and provides a highly efficient and comprehensive way to study chromatin organization during plant development, in response to different environmental stimuli, and in mutants disrupting a variety of processes, including epigenetic pathways regulating gene expression.

Diindenoperylene (DIP) and tetraphenyldibenzoperiflanthene (DBP) are two commonly used donor materials in organic solar cell devices. Despite their structural similarities, DIP films are crystalline, exhibiting good charge and exciton transport, whereas DBP films are amorphous and have lower carrier mobility and a short exciton diffusion length. However, DBP reveals a distinctly higher absorption due to the lying orientation of its transition dipole moments. In this paper, we investigate the influence of solvent vapor annealing (SVA) on the solar cell performance of both materials. In general, SVA induces a partial re-solubilization of the material leading to enhanced crystallinity of the treated layer. For DBP, extended annealing times result in a strong aggregation of the molecules, creating inhomogeneous layers unfavorable for solar cells. However, in DIP cells, SVA leads to an increase in fill factor (FF) and also a slight increase in short-circuit current density (JSC) due to interface roughening. The best results are obtained by combining solvent vapor annealed DIP layers with strongly absorbing DBP and C-70 on top. Through this device architecture, we obtain the same increase in FF in addition to a higher gain in J(SC), elevating the power conversion efficiency by a factor of 1.2 to more than 4%.

Diindenoperylene (DIP) and tetraphenyldibenzoperiflanthene (DBP) are two commonly used donor materials in organic solar cell devices. Despite their structural similarities, DIP films are crystalline, exhibiting good charge and exciton transport, whereas DBP films are amorphous and have lower carrier mobility and a short exciton diffusion length. However, DBP reveals a distinctly higher absorption due to the lying orientation of its transition dipole moments. In this paper, we investigate the influence of solvent vapor annealing (SVA) on the solar cell performance of both materials. In general, SVA induces a partial re-solubilization of the material leading to enhanced crystallinity of the treated layer. For DBP, extended annealing times result in a strong aggregation of the molecules, creating inhomogeneous layers unfavorable for solar cells. However, in DIP cells, SVA leads to an increase in fill factor (FF) and also a slight increase in short-circuit current density (JSC) due to interface roughening. The best results are obtained by combining solvent vapor annealed DIP layers with strongly absorbing DBP and C-70 on top. Through this device architecture, we obtain the same increase in FF in addition to a higher gain in J(SC), elevating the power conversion efficiency by a factor of 1.2 to more than 4%.

Diindenoperylene (DIP) and tetraphenyldibenzoperiflanthene (DBP) are two commonly used donor materials in organic solar cell devices. Despite their structural similarities, DIP films are crystalline, exhibiting good charge and exciton transport, whereas DBP films are amorphous and have lower carrier mobility and a short exciton diffusion length. However, DBP reveals a distinctly higher absorption due to the lying orientation of its transition dipole moments. In this paper, we investigate the influence of solvent vapor annealing (SVA) on the solar cell performance of both materials. In general, SVA induces a partial re-solubilization of the material leading to enhanced crystallinity of the treated layer. For DBP, extended annealing times result in a strong aggregation of the molecules, creating inhomogeneous layers unfavorable for solar cells. However, in DIP cells, SVA leads to an increase in fill factor (FF) and also a slight increase in short-circuit current density (JSC) due to interface roughening. The best results are obtained by combining solvent vapor annealed DIP layers with strongly absorbing DBP and C-70 on top. Through this device architecture, we obtain the same increase in FF in addition to a higher gain in J(SC), elevating the power conversion efficiency by a factor of 1.2 to more than 4%.

Diindenoperylene (DIP) and tetraphenyldibenzoperiflanthene (DBP) are two commonly used donor materials in organic solar cell devices. Despite their structural similarities, DIP films are crystalline, exhibiting good charge and exciton transport, whereas DBP films are amorphous and have lower carrier mobility and a short exciton diffusion length. However, DBP reveals a distinctly higher absorption due to the lying orientation of its transition dipole moments. In this paper, we investigate the influence of solvent vapor annealing (SVA) on the solar cell performance of both materials. In general, SVA induces a partial re-solubilization of the material leading to enhanced crystallinity of the treated layer. For DBP, extended annealing times result in a strong aggregation of the molecules, creating inhomogeneous layers unfavorable for solar cells. However, in DIP cells, SVA leads to an increase in fill factor (FF) and also a slight increase in short-circuit current density (JSC) due to interface roughening. The best results are obtained by combining solvent vapor annealed DIP layers with strongly absorbing DBP and C-70 on top. Through this device architecture, we obtain the same increase in FF in addition to a higher gain in J(SC), elevating the power conversion efficiency by a factor of 1.2 to more than 4%.

Diindenoperylene (DIP) and tetraphenyldibenzoperiflanthene (DBP) are two commonly used donor materials in organic solar cell devices. Despite their structural similarities, DIP films are crystalline, exhibiting good charge and exciton transport, whereas DBP films are amorphous and have lower carrier mobility and a short exciton diffusion length. However, DBP reveals a distinctly higher absorption due to the lying orientation of its transition dipole moments. In this paper, we investigate the influence of solvent vapor annealing (SVA) on the solar cell performance of both materials. In general, SVA induces a partial re-solubilization of the material leading to enhanced crystallinity of the treated layer. For DBP, extended annealing times result in a strong aggregation of the molecules, creating inhomogeneous layers unfavorable for solar cells. However, in DIP cells, SVA leads to an increase in fill factor (FF) and also a slight increase in short-circuit current density (JSC) due to interface roughening. The best results are obtained by combining solvent vapor annealed DIP layers with strongly absorbing DBP and C-70 on top. Through this device architecture, we obtain the same increase in FF in addition to a higher gain in J(SC), elevating the power conversion efficiency by a factor of 1.2 to more than 4%.

BACKGROUND The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists. RESULTS HiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq). CONCLUSIONS HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

The film morphology and device performance of planar heterojunction solar cells based on the molecular donor material α-sexithiophene (6T) are investigated. Planar heterojunctions of 6T with two different acceptor molecules, the C60 fullerene and diindenoperylene (DIP), have been prepared. The growth temperature of the 6T bottom layer has been varied between room temperature and 100 °C for each acceptor. By means of X-ray diffraction and X-ray absorption, we show that the crystallinity and the molecular orientation of 6T is influenced by the preparation conditions and that the 6T film templates the growth of the subsequent acceptor layer. These structural changes are accompanied by changes in the characteristic parameters of the corresponding photovoltaic cells. This is most prominently observed as a shift of the open circuit voltage (Voc): In the case of 6T/C60 heterojunctions, Voc decreases from 0.4 to 0.3 V, approximately, if the growth temperature of 6T is increased from room temperature to 100 °C. By contrast, Voc increases from about 1.2 V to almost 1.4 V in the case of 6T/DIP solar cells under the same conditions. We attribute these changes upon substrate heating to increased recombination in the C60 case while an orientation dependent intermolecular coupling seems to change the origin of the photovoltaic gap in the DIP case., publication date: October 27, 2014

BACKGROUND: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation capture technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalized description of nuclear organization. RESULTS: Employing circular chromosome conformation capture, this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we study the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintains a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. CONCLUSION: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: heterochromatin and euchromatin represent two distinct interactomes; interactions between chromosomes correlate with the linear position on the chromosome arm; and distal chromosome regions have a higher potential to interact with other chromosomes.