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Estrogen-related receptor beta differentially regulates target genes through diverse interactions with DNA, TFIIH, and coactivators

ABSTRACT: Estrogen-related receptor beta differentially regulates target genes through diverse interactions with DNA, TFIIH, and coactivators

PROVIDER: PRJNA803892 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17900638.fastq.gz	Fastqsanger.gz
	SRR17900639.fastq.gz	Fastqsanger.gz
	SRR17900640.fastq.gz	Fastqsanger.gz
	SRR17900641.fastq.gz	Fastqsanger.gz
	SRR17900642.fastq.gz	Fastqsanger.gz

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Project description:Estrogen-related receptor (ERR) beta is critical for maintenance of mouse embryonic stem cell (ESC) self-renewal under 2-inhibitor (“2i”) conditions. On the other hand, we biochemically revealed ERR activated transcription through the interaction with DNA, TFIIA, and C-terminal AF2 domain binding coactivators. To evaluate the biological significance of this finding, we analyzed the transcriptome of DNA-, TFIIH-, and coactivator-binding deficient mutant ERR beta-expressing ERR beta-knockout ESCs which showed compromised self-renewal activity. The results demonstrated that each interaction was required for regulating the specific biological/functional gene set among ERR beta-target genes.

2022-12-31 | GSE196202 | GEO

Progesterone Receptor Isoforms, Agonists and Antagonists Differentially Reprogram Estrogen Signaling.

Project description:Progesterone Receptor Isoforms, Agonists and Antagonists Differentially Reprogram Estrogen Signaling.

| PRJNA319518 | ENA

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

Project description:CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Few additional CDK7 substrates are known. Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase substrates in human cells. Among hundreds of high-confidence targets, the vast majority are unique to CDK7 (i.e. distinct from other transcription-associated kinases), with a subset that suggest novel cellular functions. Transcription-associated factors were predominant CDK7 substrates, including SF3B1, U2AF2, and other splicing components. Accordingly, widespread and diverse splicing defects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited cells. Combined with biochemical assays, we establish that CDK7 directly activates other transcription-associated kinases CDK9, CDK12, and CDK13, invoking a “master regulator” role in transcription. We further demonstrate that TFIIH restricts CDK7 kinase function to the RNAPII CTD, whereas other substrates (e.g. SPT5, SF3B1) are phosphorylated by the 3-subunit CDK-activating kinase (CAK; CCNH, MAT1, CDK7). These results suggest new models for CDK7 function in transcription and implicate CAK dissociation from TFIIH as essential for kinase activation. This straightforward regulatory strategy ensures CDK7 activation is spatially and temporally linked to transcription, and may apply toward other transcription-associated kinases.

2020-10-31 | GSE151699 | GEO

Systematic mutagenesis identifies p52/Tfb2 residues required for XPB/Ssl2 function within TFIIH and genetic interactions with TFB6

Project description:TFIIH is an evolutionarily conserved complex that plays central roles in both RNA polymerase II (pol II) transcription and DNA repair. As an integral component of the pol II Pre-Initiation Complex, TFIIH regulates the activity of the pol II enzyme in numerous ways. One of the essential functions of TFIIH resides in its XPB/Ssl2 subunit. XPB/Ssl2 is an ATP-dependent DNA translocase that stimulates promoter opening prior to transcription initiation. Crosslinking-mass spectrometry and cryo-EM results have shown a conserved interaction network involving XPB/Ssl2 and the C-terminal Hub region of the p52/Tfb2 core subunit. Here, we systematically mutagenized the HubA region of Tfb2 and screened for growth phenotypes in a TFB6 deletion background in Saccharomyces cerevisiae. We identified six lethal and twelve conditional mutants. Growth phenotypes of all but three of the conditional mutants were suppressed in the presence of Tfb6, thus identifying a functional interaction between Tfb2 HubA mutants and Tfb6, a protein that dissociates Ssl2 from TFIIH. Biochemical analysis of p52/Tfb2 mutants with severe growth phenotypes revealed defects in XPB/Ssl2 association. Further characterization of these Tfb2 mutant cells revealed defects in induction of Gal genes, and reduced occupancy TFIIH and pol II at Gal gene promoters, suggesting that functional TFIIH is required for proper Pol II recruitment to PICs in vivo. Consistent with recent structural models of TFIIH, our results identify key residues in the p52/Tfb2 HubA domain that are required for stable incorporation of XPB/Ssl2 into TFIIH, and for pol II transcription.

2022-06-30 | GSE196069 | GEO

Structural basis of TFIIH activation for nucleotide excision repair

Project description:Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a ‘plug’ element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway.

2019-07-02 | PXD013947 | Pride

TFIIH mutants treated with methyl methanesulfonate

Project description:Purpose of profiling experiment was to examine effects of a mutation of a subunit of TFIIH, ssl1p, which has ubiquitin ligase activity. The whole complex has previously been shown to have both kinase and helicase activities. We wanted to see if 1) there were general transcriptional defects with these mutations, as there are with other mutations to kinase activity, and 2) if there were transcriptional effects on DNA repair machinery when the mutants were treated with MMS, which is an alkylating agent. Keywords: other

2005-04-20 | GSE2343 | GEO

Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes

Project description:Transcription factors require coactivators and corepressors to modulate transcription in mammalian cells. The vitamin D receptor (VDR) utilizes coactivators and corepressors to gain tight control over the activity of a diverse set of genes that can regulate calcium transport, slow proliferation and promote immune responses. We have recently established the VDR/RXR cistrome in human colon cancer cells and have linked these binding sites to the genes that are regulated by 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). In additional studies described herein, we demonstrate that the coactivators SRC1, CBP and MED1 are recruited to upregulated genes to facilitate transcription as expected. SRC1 was the most highly correlated to VDR/RXR binding (50%). However, we also found that corepressor molecules such as NCoR and SMRT were present along with SRC1, CBP or MED1 at these 1,25(OH)2D3 activated gene enhancers. Interestingly, genome-wide NCoR binding mimicked VDR binding by increasing its association with VDR binding in response to 1,25(OH)2D3 treatment. Overall, these data indicate a complex role for corepressor and coactivator complexes in the activation or active repression of 1,25(OH)2D3 responsive genes. 5 coregulators are analyzed by ChIP-seq. The Input from GSE31939 was used as the normalizing factor for all transcription factor IPs. If lanes had more than 1 replicate, these lanes were combined for greater read depth.

2012-09-05 | E-GEOD-39277 | biostudies-arrayexpress

Ssl2/TFIIH Function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae

Project description:The initial step of RNA polymerase II (Pol II) transcription involves a large number of transcription factors and arises at multiple sites within most promoters. TFIIH is an essential, multi-subunit transcription factor that assembles on promoter DNA with Pol II and five other general transcription factors (GTFs) to form a pre-initiation complex (PIC) for basal transcription. During transcription initiation, TFIIH melts promoter DNA through the ATPase activity of its Ssl2 subunit. In the model eukaryote Saccharomyces cerevisiae, after DNA melting, Pol II scans downstream for usable transcription start sites (TSSs). To understand the function of Ssl2/TFIIH in promoter scanning and TSS selection, we identified novel alleles of SSL2 in genetic screens for mutants defective in TSS distribution that may potentially arise from altered scanning. Consistent with this notion, these ssl2 alleles alter scanning in ways that are distinct from how changes to the Pol II active site alter scanning and this difference is observed genome-wide. Our investigations support two major pathways in controlling promoter scanning and TSS selection, one controlling the efficiency of initiation through Pol II activity or factors regulating Pol II activity; another network appears to control the processivity of scanning by Ssl2/TFIIH.

2021-08-28 | GSE182792 | GEO

Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

Project description:The conserved TFIIH helicases XPB and XPD play key roles in transcription initiation and DNA repair. To investigate the functions of these helicases on a genome-wide scale, we performed ChIP-seq of endogenous XPB and XPD in the HT1080 human fibrosarcoma cell line. 2 ChIP samples and 1 unenriched input control from the same crosslinked chromatin pool

2014-02-18 | E-GEOD-44849 | biostudies-arrayexpress

Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

2014-02-18 | GSE44849 | GEO