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H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots

ABSTRACT: H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots

PROVIDER: PRJNA649545 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12265317_1.fastq.gz	Fastqsanger.gz
	SRR12265317_2.fastq.gz	Fastqsanger.gz
	SRR12265318_1.fastq.gz	Fastqsanger.gz
	SRR12265318_2.fastq.gz	Fastqsanger.gz
	SRR12265319_1.fastq.gz	Fastqsanger.gz

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H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ChIP-seq]

Project description:Although it is well established that Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that H2AK121ub marking favors a less accessible but still permissive chromatin at transcriptional regulation hotspots, which can be further reduced by EMF1 and H3K27me3. We found that when acting concurrently, H2AK121ub and H3K27me3 establish an inaccessible but responsive chromatin to marks levels, allowing gene reprograming. Conversely, when H3K27me3 is alone, chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Interestingly, despite the loss of H2AK121ub and H3K27me3 leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that gene expression is not always predictive of accessible chromatin.

2020-12-02 | GSE154696 | GEO

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ATAC-seq]

2020-12-02 | GSE154695 | GEO

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [RNA-seq]

2020-12-02 | GSE154697 | GEO

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ChIP-seq]

Project description:H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ChIP-seq]

| PRJNA647213 | ENA

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ATAC-seq]

Project description:H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ATAC-seq]

| PRJNA647212 | ENA

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [RNA-seq]

Project description:H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [RNA-seq]

| PRJNA647214 | ENA

H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-02 | GSE155378 | GEO

H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots.

Project description:Although it is well established that the Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin accessibility, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that PcG function regulates chromatin accessibility. We find that H2AK121ub is associated with a less accessible but still permissive chromatin at transcriptional regulation hotspots. Accessibility is further reduced by EMF1 acting in collaboration with PRC2 activity. Consequently, H2AK121ub/H3K27me3 marks are linked to inaccessible although responsive chromatin. In contrast, only-H3K27me3-marked chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Nevertheless, despite the loss of PcG activities leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that accessible chromatin is not always predictive of gene expression.

| S-EPMC7804394 | biostudies-literature

H2AK121ub and H3K27me3 marks have different effects on nucleosome organization in Arabidopsis

Project description:Background: Nucleosome organization within chromatin can be altered through the incorporation of histone modifications that in turn affects gene expression. Accordingly, the Polycomb Group (PcG) complexes PRC1 and PRC2 through the incorporation of H2AK121ub and H3K27me3 marks, respectively, maintain the repression of target genes; however, little is known about the exact function of these modifications in shaping nucleosome array at target genes, especially in plants. Results: By using two different MNase-seq datasets we analyzed the nucleosome occupancy profile of different PcG target genes in Arabidopsis. We found that PcG targets strongly differ in their nucleosome organization depending on the marks that they carry. Our data indicate that H2AK121ub marks play a role in fine-tuning +1 nucleosome position, while H3K27me3 marks impact nucleosome spacing and chromatin accessibility at both promoter and gene regions. Furthermore, analyzing the nucleosome profile of transcriptionally active PcG target genes in WT seedlings we found that their apparent activated state may be actually due to transcriptional heterogeneity across different cells. Conclusion: Our findings show that H2AK121ub and H3K27me3 marks differentially affect nucleosome organization in Arabidopsis, displaying additive effects when co-localizing at target genes.

2022-02-02 | GSE135978 | GEO

Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination. Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.

2015-12-07 | E-GEOD-59004 | biostudies-arrayexpress

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