Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing data of Ssu72 Wild Type and Knock-Out MEFs, hepatocytes and ES cells

ABSTRACT: To investigate how mammalian Ssu72 regulated gene expression, we performed RNA-Seq analyses of Ssu72 in three different cell types depending on their proliferation capabilities: embryonic stem (ES) cells (highly proliferating), primary murine embryonic fibroblasts (MEFs) (moderate proliferating), and hepatocytes (almost quiescent). Ssu72 deletion was induced by infection with Cre recombinase adenovius (Ad-Cre). Infection of ESf/f, MEFf/f, and hepatocytef/f with Ad-Cre resulted in efficient reduction of Ssu72 levels. Depletion of Ssu72 resulted in downregulation or upregulation of large subsets of genes in three different cell types.

ORGANISM(S): Mus musculus

PROVIDER: GSE122101 | GEO | 2020/12/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide occupanies of Ssu72, Pol II, pSer2, pSer5, pSer7 and pThr4 of Ssu72 Wild Type and Knock-out MEFs and hepatocytes

Project description:We report the genome-wide occupanies for high-throughput profiling of Pol II and Pol II CTD phosphorylation modifications in mammalian cells and tissues. By obtaining over three billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, embryonic fibroblasts and primary hepatocytes. Loss of mammalian Ssu72 was found to be related to defect of transcriptional elongation though the defects of Pol II CTD phophorylational dynamics. In addition, depletion of Ssu72 resulted in defects of Pol II elongation by reducing CTD Ser2 and Thr4 phosphorylation which induced Pol II accumulation at the proximal promoter region by increasing CTD Ser5 and Ser7 phosphorylation of transcriptionally active genes in a tissue-specific manner. Our results revealed a fundamental role of mammalian Ssu72 in regulating RNA Pol II-mediated transcriptional plasticity for cell-type-specific homeostatic maintenance.

2020-12-28 | GSE122102 | GEO

Ssu72 and Ser5P-RNAPII ChIPseq in hESCs. GROseq analysis in siCtrl and siSSu72 transfected hESCs.

2014-11-01 | GSE61393 | GEO

RNA-seq analysis in ssu72 mutant cells [WT_ssu72]

Project description:We report accumulation of cryptic antisense transcripts in ssu72 mutant cells. A histone deacetylase (Hos2) is not required to repress the cryptic transcription in SSU72+ strain however in ssu72 mutant cells, Hos2 has an important role in suppression of the cryptic transcription Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

2020-06-30 | GSE144591 | GEO

RNA-seq analysis in ssu72 and hos2 mutant cells

2020-06-30 | GSE144592 | GEO

Ssu72 and Ser5P-RNAPII ChIPseq in hESCs. GROseq analysis in siCtrl and siSSu72 transfected hESCs.

Project description:Ssu72 is a Ser5P-RNAPII phosphatase, nevertheless few targets have been characterized and its role in mammal cells remains elusive. Using ChIPseq and GROseq technologies we aimed to identify Ssu72 targets in human embryonic stem cells. For the ChIPseq experiments, H1 hESCs growing in mTeSR media were doubled fixed with DSG 2mM (45min) and FA 1% (20min) and processed to chromatin immunoprecipitation. For GROseq experiments, H1 hESCs were transfected with siCtrl or siSsu72 siRNAs using RNAimax (Invitrogene) for 48h. Then, run-on experiment was done with isolated nuclei. Nascent RNA purification and subsequent steps needed before sequencing were carried out essentially as described in Core et al, 2008, Science 319(5871): 1791-1792.

2014-11-01 | E-GEOD-61393 | biostudies-arrayexpress

Ssu72 phosphatase is essential for thermogenic adaptation by regulating cytosolic translation

Project description:Brown adipose tissue (BAT) plays a pivotal role in maintaining body temperature and energy homeostasis. To identify the fuction of Ssu72 phosphatase in BAT thermogenesis, we analyzed gene expression of BAT from SSU72 WT and SSU72aKO.

2023-02-27 | GSE224337 | GEO

Transcription profiling by tiling array of yeast ssu72, rrp6, and rco1 mutants

Project description:Genome-wide analysis of ssu72 and rrp6 mutants in Yeast

2011-05-03 | E-TABM-936 | biostudies-arrayexpress

Genome-wide maps of RNA polymerase II in WT and ssu72 mutant cells [8WG16_S2_Y1_ChIPseq]

Project description:Deletion of ssu72 gene leads to a transcription elongation defect and the increase in the level of Ser5 and Ser7 phosphorylation in CTD of Rpb1 Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

2020-06-30 | GSE144594 | GEO

Genome-wide maps of RNA polymerase II in WT and ssu72 mutant cells [S5_S7_ChIPseq]

Project description:Deletion of ssu72 gene leads to a transcription elongation defect and the increase in the level of Ser5 and Ser7 phosphorylation in carboxy-terminal domain (CTD) of Rpb1 Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

2020-06-30 | GSE144593 | GEO

RNA-seq analysis in ssu72 mutant cells [WT_ssu72]

Project description:RNA-seq analysis in ssu72 mutant cells [WT_ssu72]

| PRJNA604125 | ENA