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Using next-generation sequencing to measure the histone protein H2B and monoubiquitinated H2B (H2Bub) in single yeast cells

ABSTRACT: Using next-generation sequencing to measure the histone protein H2B and monoubiquitinated H2B (H2Bub) in single yeast cells

PROVIDER: PRJNA643412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12124800.fastq.gz	Fastqsanger.gz
	SRR12124801.fastq.gz	Fastqsanger.gz
	SRR12124802.fastq.gz	Fastqsanger.gz
	SRR12124803.fastq.gz	Fastqsanger.gz

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Using next-generation sequencing to measure the histone protein H2B and monoubiquitinated H2B (H2Bub) in single yeast cells

Project description:we report a novel strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results revealed the heterogeneities of H2B ubiquitination levels in single cells from different cell-cycle stages, which is obscured in ensemble measurements.

2020-07-02 | GSE153605 | GEO

Genome-wide maps of H2Bub and H2B states

Project description:We compare patterns of H2Bub and H2B across genes in WT, ubp8 KO and Dot1 OE cells

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Genome-wide maps of H2Bub and H2B states

Project description:Genome-wide maps of H2Bub and H2B states

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DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis

Project description:DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a plant deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.

2018-08-31 | GSE112952 | GEO

Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 tri-methylation during myogenic differentiation

Project description:Ubiquitylation of H2B on lysine 120 (H2Bub) is associated with active transcriptional elongation. H2Bub has been implicated in histone cross-talk and is generally regarded to be a prerequisite for H3K4 and H3K79 tri-methylation in both yeast and mammalian cells. We performed a genome-wide analysis of epigenetic marks during muscle differentiation, and, strikingly, we observed a near-complete loss of H2Bub in the differentiated state. We examined the basis for global loss of this mark and found that the H2B ubiquitin E3 ligase, RNF20, was depleted from chromatin in differentiated myotubes, indicating that recruitment of this protein to genes substantially decreases upon differentiation. Remarkably, during the course of myogenic differentiation, we observed retention and acquisition of H3K4 tri-methylation on a large number of genes in the absence of detectable H2Bub. The Set1 H3K4 trimethylase complex was efficiently recruited to a subset of genes in myotubes in the absence of detectable H2Bub, accounting in part for H3K4 tri-methylation in myotubes. Our studies suggest that H3K4me3 deposition in the absence of detectable H2Bub in myotubes is mediated via Set1 and, perhaps, MLL complexes, whose recruitment does not require H2Bub. Thus, muscle cells represent a novel setting in which to explore mechanisms that regulate histone cross-talk. Mapping of H2Bub in growing myoblasts (MB) and fully differentiated myotubes (MT).

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Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 tri-methylation during myogenic differentiation

2012-03-06 | GSE34960 | GEO

Genome-wide maps of H3K79me and H2Bub states

Project description:We compare patterns of H3K79me and H2Bub across genes in budding yeast

2019-06-13 | GSE107331 | GEO

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis [ChIP-seq]

2018-08-31 | GSE112951 | GEO

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis [RNA-seq]

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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

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