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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE155378 | GEO | 2020/12/02

REPOSITORIES: GEO

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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 in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [RNA-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 | GSE154697 | GEO

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

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

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

| PRJNA649545 | 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 [ChIP-seq]

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

| PRJNA647213 | ENA

Regulation of the boundaries of accessible chromatin.

Project description:Regulatory regions maintain nucleosome-depleted, open chromatin status but simultaneously require the presence of nucleosomes for specific histone modifications. It remains unclear how these can be achieved for proper regulatory function. Here we demonstrate that nucleosomes positioned within accessible chromatin regions near the boundaries provide platforms for histone modifications while preventing the occlusion of regulatory elements. These boundary nucleosomes were particularly enriched for active or poised regulatory marks in human, such as histone acetylations, H3K4 methylations, H3K9me3, H3K79me2, and H4K20me1. Additionally, we found that based on a genome-wide profiling of ~100 recombinant yeast strains, the location of open chromatin borders tends to vary mostly within 150 bp upon genetic perturbation whereas this positional variation increases in proportion to the sequence preferences of the underlying DNA for nucleosome formation. More than 40% of the local boundary shifts were associated with genetic variation in cis- or trans-acting factors. A sizeable fraction of the identified genetic factors was also associated with nearby gene expression, which was correlated with the distance between the transcription start site (tss) and the boundary that faces the tss. Taken together, the variation in the width of accessible chromatin regions may arise in conjunction with the modulation of the boundary nucleosomes by post-translational modifications or by chromatin regulators and in association with the activity of nearby gene transcription.

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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Project description:Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

| S-EPMC5862073 | biostudies-literature

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