FACT-mediated depletion of macroH2A-nucleosome regulates the cell response of macrophage
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ABSTRACT:
PROVIDER: PRJNA1044766 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26941500_1.fastq.gz | Fastqsanger.gz | |||
| SRR26941500_2.fastq.gz | Fastqsanger.gz | |||
| SRR26941501_1.fastq.gz | Fastqsanger.gz | |||
| SRR26941501_2.fastq.gz | Fastqsanger.gz | |||
| SRR26941502_1.fastq.gz | Fastqsanger.gz |
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Project description:The histone variant macroH2A has been shown to generally associate with transcriptionally silent chromatin states. However, how macroH2A regulates the chromatin structure and functions in transcriptional process still remains elusive at the molecular level. In this study, we demonstrate that the incorporation of macroH2A does not affect the stability and the folding dynamics of nucleosome, but greatly impairs the FACT’s maintenance function at the nucleosome level. FACT can greatly impair the stability of macroH2A nucleosome, and quickly deplete the macroH2A nucleosome after the first unfolding process. Furthermore, we identify the key residue S139 of macroH2A, whose mutation can rescue the FACT’s function to maintain nucleosome integrity. Genome-wide analyses show that S139 mutation in macroH2A reshapes the position of macroH2A and regulates the stimulation-induced transcription in macrophage. Our findings provide mechanistic insights of how histone variant macroH2A coregulates with FACT at the nucleosome level and functions in cell response of macrophage in immunity.
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Project description:Mammalian genomes are organized into distinct chromatin structures, which include small-scale nucleosome arrays and large-scale topologically associating domains (TADs). The mechanistic interplay between chromatin structures across scales is poorly understood. Here, we investigate how changes in nucleosome architecture impact TAD organization by studying the role of the histone chaperone facilitates chromatin transcription (FACT) in 3D genome organization. We show that FACT depletion perturbs TADs, causing decreased insulation and weaker CTCF loops. These changes in TAD structure cannot be attributed to changes in chromatin occupancy of CTCF or cohesin and occur specifically in transcribed regions of the genome where we observe perturbed nucleosome organization in absence of FACT. FACT depletion therefore allows us to separate the role of CTCF binding from nucleosome architecture and to demonstrate that the organization of nucleosomes at TAD boundaries directly contributes to TAD formation.
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Project description:FACT depletion demonstrates a role for nucleosome organization in TAD formation
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Project description:FACT depletion demonstrates a role for nucleosome organization in TAD formation [1]
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Project description:The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion. Examination of transcription factor occupancy in cells with newly synthesized Oct4.
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Project description:Genetic loss-of-function studies in development, cancer and somatic cell reprogramming have suggested that the group of macroH2A histone variants might function through stabilizing the differentiated state by a yet unknown mechanism. Here, we present results demonstrating that macroH2A variants have a major function in maintaining nuclear organization and heterochromatin architecture. Specifically, we find that a substantial amount of macroH2A is associated with heterochromatic repeat sequences. We further identify macroH2A on sites of interstitial heterochromatin decorated by H3K9me3. Loss of macroH2A leads to major defects in nuclear organization including reduced nuclear circularity, disruption of nucleoli and a global loss of dense heterochromatin. Domains formed by repeat sequences when depleted of macroH2A are disorganized, expanded and fragmented and mildly re-expressed. On the molecular level we find that macroH2A is required for the interaction of repeat sequences with the nucleostructural protein Lamin B1. Taken together our results argue that a major function of macroH2A histone variants is to link nucleosome composition to higher order chromatin architecture.
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