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Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [RNA-seq]

ABSTRACT: Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [RNA-seq]

PROVIDER: PRJNA698730 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13594931_1.fastq.gz	Fastqsanger.gz
	SRR13594931_2.fastq.gz	Fastqsanger.gz
	SRR13594932_1.fastq.gz	Fastqsanger.gz
	SRR13594932_2.fastq.gz	Fastqsanger.gz
	SRR13594933_1.fastq.gz	Fastqsanger.gz

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Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.

Project description:Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.

| PRJNA698518 | ENA

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [ChIP-seq]

Project description:Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [ChIP-seq]

| PRJNA698733 | ENA

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [RNA-seq]

Project description:Chromatin remodeling plays very important role in cell reprogramming, but its underlying mechanism remains poorly understood. Here, we show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the other two stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene network establishment. Our results not only uncover a previously unknown function of RNF20-mediated H2B ubiquitination in cell reprogramming, but also provide mechanistic insights into the epigenetic regulation of reprogrammable cells.

2021-02-02 | GSE165886 | GEO

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [ChIP-seq]

Project description:Chromatin remodeling plays very important role in cell reprogramming, but its underlying mechanism remains poorly understood. Here, we show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the other two stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene network establishment. Our results not only uncover a previously unknown function of RNF20- mediated H2B ubiquitination in cell reprogramming, but also provide mechanistic insights into the epigenetic regulation of reprogrammable cells.

2021-02-02 | GSE165885 | GEO

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.

Project description:ObjectivesCell reprogramming has significant impacts on their potential application in regenerative medicine. Chromatin remodelling plays a very important role in cell reprogramming, but its underlying mechanism remains poorly understood.Materials and methodsRNA-seq, quantitative RT-PCR and western blot analysis were applied to study the role of RNF20 and H2B ubiquitination during mouse somatic cell reprogramming. Chromatin structure and the recruitment of transcription factors were analysed by ChIP-seq, micrococcal nuclease sensitivity assays and immunofluorescence staining.ResultsWe show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the maturation and stabilization stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene network establishment.ConclusionsHistone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.

| S-EPMC8349662 | biostudies-literature

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.

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

2021-02-02 | GSE165887 | GEO

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

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

2013-07-28 | GSE38099 | GEO

The Mediator complex subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination

Project description:The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23-/- (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chromatin. In a cell-free system, Mediator directly and substantially increases H2Bub on recombinant chromatin through its cooperation with RNF20/40 and the PAF complex. Integrative genome-wide analyses show that MED23 depletion specifically reduces H2Bub on a subset of MED23-contolled genes. Importantly, MED23-coupled H2Bub levels are oppositely regulated during myogenesis and lung carcinogenesis. In sum, these results establish a mechanistic link between the Mediator complex and a critical chromatin modification in coordinating transcription with cell growth and differentiation. To examine the enrichment of H2B ubiquitination, Pol II, H3K4me3, H3K79me3 in WT and KO MED23 MEF cells, we performed H2Bub ChIP-seq, Pol II ChIP-seq, H3K4me3 ChIP-seq and H3K79me3 ChIP-seq assays. 10 high-throughput sequencing data were deposited and WT, KO input data were controls for peak calling.

2015-09-16 | E-GEOD-59518 | biostudies-arrayexpress

Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination

Project description:Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination

| PRJNA308071 | ENA