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Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [RNA-Seq]

ABSTRACT: Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [RNA-Seq]

PROVIDER: PRJNA643265 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12121523.fastq.gz	Fastqsanger.gz
	SRR12121524.fastq.gz	Fastqsanger.gz
	SRR12121525.fastq.gz	Fastqsanger.gz
	SRR12121526.fastq.gz	Fastqsanger.gz
	SRR12121527.fastq.gz	Fastqsanger.gz

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Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [RNA-Seq]

Project description:The deubiquitinating module (DUBm) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and ATXN7, ATXN7L3 and ENY2 adaptor proteins, which are all needed for the full activity of USP22 enzyme. In addition, ATXN7L3 is critical for directing the DUB module substrate specificity towards H2Bub1. We reported that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, while in contrast H2Bub1 levels were strongly increased in Atxn7l3 null mutants and derived cellular systems. Interestingly, the strong H2Bub1 increases observed in the Atxn7l3-/- mouse embryonic stem cells, or Atxn7l3-/- mouse embryonic fibroblasts, do not correlate with the modest genome-wide Pol II occupancy changes observed in the two knock-out cellular systems. Thus, histone H2Bub1 deubiquitylation does not directly regulate global RNA polymerase II transcription.

2021-02-16 | GSE153578 | GEO

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [ChIP-Seq]

2021-02-16 | GSE153584 | GEO

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA

Project description:Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA

| PRJNA643273 | ENA

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [ChIP-Seq]

Project description:Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [ChIP-Seq]

| PRJNA643279 | ENA

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription.

Project description: Not available

| S-EPMC8329007 | biostudies-literature

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA

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

2021-02-16 | GSE153587 | GEO

The H2Bub1-deposition complex is required for human and mouse cardiogenesis (RNA-Seq)

Project description:De novo variants affecting monoubiquitination of histone H2B (H2Bub1) are enriched in human congenital heart disease. H2Bub1 is required in stem cell differentiation, cilia function, post-natal cardiomyocyte maturation, and transcriptional elongation. However, how H2Bub1 affects cardiogenesis is unknown. We show that the H2Bub1-deposition complex (RNF20-RNF40-UBE2B) is required for mouse cardiogenesis and for differentiation of human iPSCs into cardiomyocytes. Mice with cardiac-specific Rnf20 deletion are embryonic lethal and have abnormal myocardium. We then analyzed H2Bub1 marks during differentiation of human iPSCs into cardiomyocytes. H2Bub1 is erased from most genes at transition from cardiac mesoderm to cardiac progenitor cells, but is preserved on a subset of long cardiac-specific genes. When H2Bub1 is reduced in iPSC-cardiomyocytes, long cardiac-specific genes have fewer full-length transcripts. This correlates with H2Bub1 accumulation near the center of these genes. H2Bub1 accumulation near the center of tissue-specific genes was also observed in embryonic fibroblasts and fetal osteoblasts. In summary, we show that normal H2Bub1 distribution is required for cardiogenesis and cardiomyocyte differentiation, and point to H2Bub1 regulating tissue-specific gene expression by increasing the amount of full-length transcripts.

2023-10-31 | GSE246411 | GEO

Transcriptom modulated by LDOC1 / H2Bub1 axis

Project description:Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is one of the prominent epigenetic marks that regulates multiple cellular processes, including immunity, stem cell differentiation, tumorigenesis, and DNA damage response, mainly through affecting transcription of specific gene sets. The Ring Finger Protein 40 (RNF40) and its paralog RNF20 forms a stable E3 ligase heterodimer is the major enzymatic complex responsible for H2B monoubiquitylation. Dysregulation of H2Bub1 was observed in early stage of non-small cell lung carcinoma (NSCLC). However, the underlying regulatory mechanism and the impact of aberrant H2Bub1 level in the metastasis and chemotherapy response of NSCLC patients remains unelucidated. We found LDOC1 associated with RNF40 in NSCLC A549 cells. In this study, we investigate the role of LDOC1 in epigenome and aggressiveness of NSCLC involving H2Bub1.

2026-06-30 | GSE246303 | GEO

Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription

Project description:Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both are enriched in coding regions, and H2Bub1 levels are directly proportional to those of phospho-Spt5. Cdk9-dependence of antisense suppression correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Combined reduction of Cdk9 activity and loss of H2Bub1 prevent recruitment of the histone deacetylase Clr6-CII to transcribed genes, and lead to decreased histone occupancy and increased histone acetylation within gene coding regions. These results uncover new pathways linking regulators of RNAPII transcription elongation to suppression of aberrant antisense transcription, and demonstrate novel interactions between co-transcriptional histone modification pathways.

2020-05-21 | GSE115682 | GEO

The H2Bub1-deposition complex is required for human and mouse cardiogenesis (ChIP-Seq)

2023-10-31 | GSE246410 | GEO