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The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [RNA-seq]

ABSTRACT: The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [RNA-seq]

PROVIDER: PRJNA511350 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8352490.fastq.gz	Fastqsanger.gz
	SRR8352491.fastq.gz	Fastqsanger.gz
	SRR8352492.fastq.gz	Fastqsanger.gz
	SRR8352493.fastq.gz	Fastqsanger.gz
	SRR8352494.fastq.gz	Fastqsanger.gz

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The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [MNase-seq]

Project description:The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA Polymerase II passage through chromatin. It remains unknown to what extent they cooperate in vivo. Here, we used genome-wide, genetic, biochemical and microscopic approaches to dissect their interplay in the fission yeast Schizosaccharomyces pombe. We show that FACT and H2Bub repress antisense transcripts near the 5’ end and inside gene bodies, respectively. The accumulation of these transcripts accompanies with changes at genic nucleosomes in FACT and H2Bub mutants. Moreover, in the H2Bub mutant, FACT binding to histones is stabilized. Interestingly, analysis of FACT-H2Bub double mutants revealed that FACT depletion suppresses genic nucleosome loss in the H2Bub mutant. In addition, FACT, unlike H2Bub, maintains nucleosomes in intergenic regions. This is especially important for subtelomeric gene repression and in compacting chromatin into ‘knobs’. Collectively, our study demonstrates that FACT and H2Bub functionally interact with each other in a genome-context dependent manner. Further, our data indicate an involvement of FACT in higher order chromatin formation outside of euchromatin.

2019-12-11 | GSE124091 | GEO

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [RNA-seq]

2019-12-11 | GSE124090 | GEO

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [ChIP-Seq]

2019-12-11 | GSE135766 | GEO

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions

Project description:The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions

| PRJNA510892 | ENA

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [MNase-seq]

Project description:The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [MNase-seq]

| PRJNA511349 | ENA

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [ChIP-Seq]

Project description:The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [ChIP-Seq]

| PRJNA560030 | ENA

The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions.

Project description:The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA polymerase II (Pol II) passage through chromatin, yet it is not clear how they cooperate mechanistically. We used genomics, genetic, biochemical, and microscopic approaches to dissect their interplay in Schizosaccharomyces pombe. We show that FACT and H2Bub globally repress antisense transcripts near the 5' end of genes and inside gene bodies, respectively. The accumulation of these transcripts is accompanied by changes at genic nucleosomes and Pol II redistribution. H2Bub is required for FACT activity in genic regions. In the H2Bub mutant, FACT binding to chromatin is altered and its association with histones is stabilized, which leads to the reduction of genic nucleosomes. Interestingly, FACT depletion globally restores nucleosomes in the H2Bub mutant. Moreover, in the absence of Pob3, the FACT Spt16 subunit controls the 3' end of genes. Furthermore, FACT maintains nucleosomes in subtelomeric regions, which is crucial for their compaction.

| S-EPMC7007867 | biostudies-literature

The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions

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

2019-12-11 | GSE124092 | GEO

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

Project description:Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A-H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A-H2B deposition by FACT. 6 samples, 2 inputs and 4 ChIP samples for histone H2B (2 for wild-type and 2 for an H2B â30-37 mutant)

2016-08-10 | E-GEOD-80831 | biostudies-arrayexpress

Examination of histone H2B ubiquitination in wild type and USP49 knockdown cells [ChIP-Seq]

Project description:Posttranslational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of USP49 as a histone H2B specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient co-transcriptional splicing of a large set of exons. USP49 forms a complex with RVB1 and SUG1, and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression, but affects the abundance of over 9,000 isoforms. Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency. Importantly, USP49 is relatively enriched at this set of exons. USP49 knockdown increased uH2B levels at these exons as well as upstream 3’ and downstream 5’ intronic splicing elements. Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B specific deubiquitinase and uncovers a critical role for H2B deubiquitination in co-transcriptional pre-mRNA processing events. Examination of histone H2B ubiquitination in wild type and USP49 knockdown cells [ChIP-Seq]

2013-07-28 | E-GEOD-38099 | biostudies-arrayexpress

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