Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA736615 | ENA |
REPOSITORIES: ENA
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Project description:We studied how H1 regulates higher-order chromatin architecture by performing Hi-C. In addition, we tested the effects of H1 domains on nucleosome organisation and DNA methylation by performing MNase-seq and Bisulfite-seq.
2024-02-15 | GSE176526 | GEO
Project description:In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create an h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.
2021-03-26 | GSE146948 | GEO
Project description:Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs
| PRJNA948378 | ENA
Project description:Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.
2024-04-23 | GSE228140 | GEO
Project description:Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.
2024-04-23 | GSE228076 | GEO
Project description:Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.
2024-04-23 | GSE228067 | GEO
Project description:Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.
2024-04-23 | GSE249374 | GEO
Project description:Chromosomal RNAs (cRNAs) are a poorly understood fraction of cellular RNAs that co-purify with chromatin. Here we show that, in Drosophila, cRNAs constitute a heterogeneous group of RNA species that cover ~28% of the genome. Intriguingly, we found that cRNAs are highly enriched in heterochromatic transcripts. Our results show that heterochromatic cRNAs interact with the hnRNP A/B proteins hrp36 and hrp48 to assemble into RNP particles. We also show that depletion of linker histone dH1, a major component of chromatin, impairs assembly of hrp36 and hrp48 onto heterochromatic cRNAs. Concomitantly, impaired cRNAs assembly induces the accumulation of heterochromatic cRNAs and the formation of unscheduled RNA::DNA hybrids (R-loops). Linker histones H1 are known to regulate chromatin structure and compaction and, indeed, we show that dH1 depletion perturbs chromatin organization, reducing nucleosome occupancy and specifically increasing accessibility and 3D interactions within heterochromatin. These perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loops formation and cRNAs retention at heterochromatin. Altogether, these results unveil the unexpected contribution of linker histones to RNPs assembly and homeostasis of cRNAs.
2024-04-23 | GSE228068 | GEO
Project description:Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. Here we show that without histone H1, RdDM enters heterochromatin, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.
2021-12-01 | GSE179796 | GEO
Project description:The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, our understanding of how the chromatin is organized to prohibit the reversal of the developmental program remains limited. Specifically, the totipotency to pluripotency transition marks one of the most dramatic events to the chromatin, yet the nature of histone changes and regulation underlying this process are only partly characterized. Here we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Further, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress totipotency in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in mediating chromatin repression and desolation of the totipotent identity.
2021-10-22 | GSE153040 | GEO