Biology subjects

Barneche, F.

Publications and source records attributed to Barneche, F..

15 recordsLinked to original sources

bioRxiv2026

GH1-HMGA proteins restrict RNA-directed DNA methylation and antagonize linker histone H1 at euchromatic transposable elements

In plant genomes, transposable elements (TEs) are silenced by CG and non-CG DNA methylation, with non-CG methylation maintained by CMT chromomethylases and the RNA-directed DNA methylation (RdDM) pathway. In Arabidopsis, linker histone H1 differentially influences these pathways, as loss of H1 causes non-CG hypermethylation at pericentromeric TEs but hypomethylation at euchromatic TEs in gene-rich regions. The molecular basis of this antagonism has remained unclear. Here, we show that GH1-HMGAs, a family of H1-related High Mobility Group proteins, bind AT-rich sequences at euchromatic TEs and prevent RdDM-dependent non-CG methylation by limiting siRNA accumulation. Furthermore, GH1-HMGA and H1 compete for chromatin association at these TEs, as loss of GH1-HMGA triggers ectopic H1 redistribution, while loss of H1 increases GH1-HMGA enrichment, providing a mechanistic explanation for the non-CG hypomethylation observed in h1 mutants. Collectively, these findings reveal how GH1-HMGA proteins specifically restrain RdDM activity at euchromatic TEs and elucidate how the H1/GH1-HMGA balance spatially partitions distinct DNA methylation pathways across the genome.

genetics↗

bioRxiv2026

Centromeric origin of Arabidopsis interstitial telomeric repeat domains

The mechanisms underlying the emergence of new DNA repeat classes remain poorly understood. One such example is the formation of interstitial telomeric repeat (ITR) domains commonly viewed as telomere-fossil byproducts of chromosome rearrangements. Here, we report that in Arabidopsis thaliana, ITRs arise from centromeres as centromeric-telomeric mosaic satellites that expand into higher-order structures via in situ amplification. Long-read sequencing of mutation accumulation lines and forward simulations of mutational processes confirmed the propensity of centromeres to form telomeric motifs. During establishment, ITRs adopt an atypical chromatin state that excludes CENH3 incorporation, thereby enabling escape from the functional constraints of centromere identity. Accordingly, a pangenomic survey of natural accessions showed that ITRs vary abruptly and independently of telomere length, notably through transposon-associated block duplications. These findings identify centromeres as major sources of telomeric sequences and an original route for the emergence of new DNA satellite types.

genomics↗

bioRxiv2025

Linker Histones Enhance Robustness in Diurnal Transcription Dynamics.

Linker histone H1 is crucial for chromatin organization and gene expression in Arabidopsis thaliana, influencing development and stress responses. To explore its role in diurnal gene regulation, we examined H1-deficient plants and found that H1 is essential for maintaining rhythmic gene expression. Genes losing synchronization often contained NAC transcription factor binding sites, indicating H1 may affect their accessibility. Nuclear imaging revealed that H1 subtly modulates nuclear size and chromatin distribution across the photoperiod. Epigenetic analysis showed typical diurnal changes--declines in H3K4me3 and active RNA Pol II in the evening and increases in H3K27me3. In H1 mutants, these patterns persisted but with elevated H3K4me3 and RNA Pol II (Ser2P) levels at night and in the morning. These results suggest that H1 fine-tunes chromatin and transcriptional rhythms, contributing to the temporal coordination of gene activity in response to environmental and developmental signals.

plant biology↗

bioRxiv2025

Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control

Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for survival and therefore represent excellent models to understand the diversity of gene regulatory mechanisms, yet chromatin-based mechanisms have never been explored in these organisms. In this study, we combined genome-wide profiling of histone and DNA modifications with transcriptomic analyses of the marine polar diatom Fragilariopsis cylindrus upon entry and exit of a 3-month-long polar night. We show that, in agreement with its established role in transcription facilitation, histone H2B monobiquitination (H2Bub) is modulated at active genes upon prolonged darkness to light re-exposure. In contrast, histone H3 lysine 27 trimethylation (H3K27me3) and DNA cytosine methylation (CG methylation), two modifications typically associated with the silencing of genes or transposable elements (TEs), remained stable throughout the transitions, reinforcing their role in transcriptional repression, particularly at TEs but also at a few genes. We further demonstrate that H3K27me3 and DNA methylation are physically associated at TEs, probably reflecting a dual locking system enabling F.cylindrus cells to cope with the invasive nature of these genetic elements under extreme environmental conditions. These findings enhance our understanding of genome and epigenome regulation in diatoms in response to environmental variability and open new avenues for exploring the role played by chromatin-level regulation in the unique evolutionary history of polar unicellular eukaryotes.

genomics↗

bioRxiv2025

Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

Plant photomorphogenesis is a light-induced developmental switch that combines massive reprogramming of gene expression and a general enhancement in RNA Polymerase II activity. Yet, transcriptome analyses have failed to demonstrate a clear tendency toward gene upregulation. To solve this conundrum, we optimized a spike-in RNA-seq experimental and analysis pipeline and reconciled transcriptome dynamics with epigenomic and cytogenetic observations. We found that light induces a two-fold expansion of the transcriptome during Arabidopsis thaliana cotyledon photomorphogenesis, with 94% of the 9,128 differentially expressed genes being upregulated within the first six hours. Transcriptome augmentation was further detected at a similar strength in spike-free RNA-seq datasets from independent laboratories renormalized using stable genes that mimic the spike-in information. On this new basis, reinterpretation of light-mediated gene regulatory pathways revealed a quasi-exclusive positive effect of HY5 and other key light-induced transcription factors at target genes. This new standpoint unveiled the unilateral impact of light on the transcriptome of Arabidopsis cotyledons at the genome scale and opens new avenues for investigating global genome regulation during plant developmental and environmental responses.

plant biology↗

bioRxiv2023

Genome-wide evidence of the role of Paf1C in transcription elongation and histone H2B monoubiquitination in Arabidopsis

The evolutionarily conserved Paf1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNAPII progression through chromatin remodeling. To obtain evidence that Paf1C acts in transcription elongation in Arabidopsis, we examined the genomic distribution of the ELF7 and VIP3 subunits of Paf1C. The occupancy of both subunits was confined to thousands of gene bodies and positively correlated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome-wide in elf7 seedlings. Genome-wide profiling of RNAPII revealed that in elf7 mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest that there is a direct functional link between Paf1C activity, mono-ubiquitination of histone H2B, and the transition of RNPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stably than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.

plant biology↗

bioRxiv2023

Distinct clades of TELOMERE REPEAT BINDING transcriptional regulators interplay to regulate plant development

TELOMERE REPEAT BINDING proteins (TRBs) are plant-specific transcriptional regulators that combine two DNA-binding domains, the GH1 domain shared with H1 histones that binds to linker DNA and the Myb/SANT domain that specifically recognizes the telobox DNA binding site motif. TRB1, TRB2 and TRB3 proteins recruit the Polycomb group complex 2 (PRC2) to deposit H3K27me3 and JMJ14 to remove H3K4me3 at target genes containing telobox motifs in their promoters to repress transcription. Here, we characterize the function of TRB4 and TRB5, which belong to a separate TRB clade conserved in spermatophytes. TRB4 and TRB5 affect the transcriptional control of several hundred genes involved in developmental responses to environmental cues, the majority of which differ from differentially regulated genes in trb1 trb2 trb3, suggesting distinct modes of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly at TSS and promoter regions of transcriptionally active and H3K4me3-marked genes but is not enriched at H3K27me3-marked gene bodies. TRB4 physically interacts with the PRC2 component CURLY LEAF (CLF), but, unexpectedly, loss of TRB4 and TRB5 partially suppresses the developmental defects of clf mutant plants, by acting as transcriptional activators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, collectively unveiling that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.

plant biology↗

bioRxiv2023

A layer cake model for plant and metazoan chromatin

Early structural studies of chromosome organisation in eukaryotic nuclei led to the identification of euchromatin and heterochromatin, two main archetypes of chromatin visible through microscopy. Subsequently, the diversity of chromatin composition along the linear genome sequence was resolved using high throughput sequencing techniques to map a multitude of chromatin marks and unravel their functional organisation. Recent analyses of human chromosome conformation capture experiments tend to point to the existence of several chromosome sub-compartments that may correspond to epigenomic variations in chromatin composition. Here, we compare genome 3D organisations in representative eukaryotic species to explore the links between chromosomal sub-compartments and chromatin marks, genome replication timing, and genomic repeats in six model organisms, including vertebrates, plants and insects. We report that the 3D organisation of chromatin in organisms with different genome content and size can be described as layers characterised by distinct chromatin marks and activities. We propose a "layer cake" model for the genome 3D organisation as a more refined view than the prevalent "two compartments" model of chromatin organisation in multi-cellular organisms.

genomics↗

bioRxiv2022

The UBP5 histone H2A deubiquitinase counteracts PRC2-mediated repression to regulate Arabidopsis development and stress responses

Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. However, there is limited knowledge about PRCs interacting proteins and their interplay with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a novel interactor of the PRC2 subunit SWINGER and its associated factor PWO1 in Arabidopsis thaliana. As inferred from the functional analyses of ubp5 CRISPR-Cas9 mutant plants, UBP5 regulates plant development and stress responses, notably by promoting H2A monoubiquitination erasure, leading to transcriptional de-repression. Preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants further suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, UBP5 provides novel insights to disentangle the complex PRC2 interaction network and is a crucial regulator of the pivotal epigenetic repressive marks H2Aub and H3K27me3.

developmental biology↗

bioRxiv2020

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

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 first report 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 unveils a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/402172v5_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13cf29dorg.highwire.dtl.DTLVardef@5c5c86org.highwire.dtl.DTLVardef@1be7516org.highwire.dtl.DTLVardef@f935cb_HPS_FORMAT_FIGEXP M_FIG Teano et al. report that that linker histone H1 and a group of H1-related telomeric proteins interplay to selectively influence the Polycomb repressive landscape at genes and telomeric repeats in Arabidopsis. These findings provide a mechanistic framework by which H1 influences the epigenome and nuclear organization in a sequence-specific manner. C_FIG HighlightsO_LIH1 promotes PRC2 activity and limits accessibility at a majority of genes C_LIO_LIH1 prevents PRC2 activity at telomeric DNA sequences C_LIO_LIPRC2 repression is achieved by restricting accessibility to TRB proteins C_LIO_LIH1 orchestrates the spatial organization of telomeres and interstitial telomeres (ITRs) C_LI

molecular biology↗

bioRxiv2020

DET1-mediated COP1 regulation avoids HY5 activity over second-site targets to tune plant photomorphogenesis

DE-ETIOLATED1 (DET1) is a negative regulator of plant photomorphogenesis acting as a component of the C3D complex, which can further associate to CULLIN4 to form a CRL4C3D E3 ubiquitin ligase. CRL4C3D is thought to act together with CRL4COP1SPA ubiquitin ligase, to promote the ubiquitin-mediated degradation of the master regulatory transcription factor ELONGATED HYPOCOTYL5 (HY5), thereby controlling photomorphogenic gene regulatory networks. Yet, functional links between COP1 and DET1 have long remained elusive. Here, upon mass spectrometry identification of DET1 and COP1-associated proteins, we provide in vivo evidence that DET1 associates with COP1 to promote its destabilization, a process necessary to dampen HY5 protein abundance. By regulating HY5 over-accumulation, DET1 is critical to avoid its association to second-site loci, including many PIF3 target genes. Accordingly, excessive HY5 levels result in an increased HY5 repressive activity and are sufficient to trigger fusca-like phenotypes otherwise observed typically in COP1 and COP9 signalosome mutant seedlings. This study therefore identifies that DET1-mediated regulation of COP1 stability tunes down HY5 cistrome and avoids hyper-photomorphogenic responses that might compromise plant viability.

plant biology↗

bioRxiv2019

Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading into euchromatic islands

The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically downregulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some TE loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine (SAM) synthase MAT3, which is required for H3K9me2 deposition. Topoisomerase VI promotes MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a mechanistic insight into the essential role of Topoisomerase VI in the delimitation of chromatin domains.

plant biology↗

bioRxiv2019

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a high-molecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.

plant biology↗

bioRxiv2018

Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis

Chromatin in eukaryotes provides a tunable platform to control gene expression and convey an epigenetic memory throughout cell divisions. H1 linker histones are abundant components with an intrinsic potential in influencing chromatin structure and function. We detail the impact of H1 depletion in Arabidopsis on fine-scale chromatin organization, transcription and development. While required for chromocenter assembly, H1s are dispensable for transposable element (TE) silencing and peripheral positioning of heterochromatin. In euchromatin, H1 regulates nucleosome density, mobility, and regular distribution of nanoscale chromatin domains. While necessary to maintain epigenetic patterns, H1 only moderately affects transcription. Its depletion is associated with failures in transitional fate changes such as lateral root initiation, root hair production, stomata patterning but also flowering and dormancy regulation. Therefore, Arabidopsis H1 variants are chromatin architects mediating nano- and microscale levels-of-organization operating downstream of epigenetic and transcriptional establishment processes and contribute to epigenetic reorientations in developmental transitions.

molecular biology↗

bioRxiv2018

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a plant deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.

plant biology↗