Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA259205 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation at transcription start sites blocks TBP binding and transcription onset by RNApolII
| PRJNA259204 | ENA
Project description:DNA methylation at transcription start sites blocks TBP binding and transcription onset by RNApolII [MeDIP]
| PRJNA259206 | ENA
Project description:Aim: To determine the state of methylation of DNA molecules that are physically engages with either poised or active enhancers. Methods: We used ChIP-bisulfite-sequencing with H3K4me1 antibody to map the methylation of DNA bound to enhancer. We used ChIP-sequencing with RNApolII-PS5 antibody to map actively transcribing transcription start sites. We used reduced representation bisulfite sequencing (RRBS) to map total DNA methylation. Results - conclusion: DNA molecules that are physically found in H3K4me1 chromatin are hypomethylated while DNA found in enhancers that are associated with active transcription is further demethylated.
2018-04-11 | GSE98549 | GEO
Project description:The TATA binding protein (TBP) is a transcription factor that binds specifically to a DNA sequence called the TATA box upstream of the transcription start site. To gain insight into the genes occupied by TBP, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against TBP.
2010-06-15 | E-GEOD-22303 | biostudies-arrayexpress
Project description:The TATA binding protein (TBP) is a transcription factor that binds specifically to a DNA sequence called the TATA box upstream of the transcription start site. To gain insight into the genes occupied by TBP, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets.
2010-06-15 | GSE22303 | GEO
Project description:General transcription factor TFIID is a key component of RNA polymerase II transcription initiation in eukaryotic nuclei. Human TFIID is a megadalton-sized multiprotein complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. A number of transcription regulatory factors were found to compete with DNA for TBP binding. We identified a ternary complex formed by TBP and the histone fold (HF) domain containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1. In an integrative approach combing crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. Our results thus suggest a novel regulatory state for TFIID function.
2017-11-15 | PXD005676 | Pride
Project description:Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. We used CXMS to study the organization and structure of the purified TFIID complex from Komagataella phaffii. Together with Cryo-EM, We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a HF domain. Interaction with promoter DNA highlights two non-selective binding sites consistent with a DNA scanning mode.
2018-10-08 | PXD011092 | Pride
Project description:The Swi2/Snf2-family ATPase Mot1 displaces TBP from DNA in vitro, but the global relationship between Mot1 and TBP in vivo has been unclear. We therefore mapped the distribution of Mot1 and TBP on native chromatin at base-pair resolution. Mot1 and TBP binding sites coincide throughout the genome, and depletion of TBP results in a global decrease in Mot1 binding. Using midpoint-versus-length mapping to assess the spatial relationship of Mot1 and TBP on chromatin, we find evidence that Mot1 approaches TBP from the upstream direction, consistent with its in vitro mode of action. Strikingly, inactivation of Mot1 leads to both increases and decreases in TBP-genome association. Sites of TBP gain tend to contain robust TATA boxes, while sites of TBP loss contain poly(dA:dT) tracts that may contribute to nucleosome exclusion. We propose that the action of Mot1 is required to clear TBP from intrinsically preferred (TATA-containing) binding sites, ensuring sufficient soluble TBP to bind intrinsically disfavored (TATA-less) sites.
2013-10-21 | GSE44200 | GEO
Project description:The Swi2/Snf2-family ATPase Mot1 displaces TBP from DNA in vitro, but the global relationship between Mot1 and TBP in vivo has been unclear. We therefore mapped the distribution of Mot1 and TBP on native chromatin at base-pair resolution. Mot1 and TBP binding sites coincide throughout the genome, and depletion of TBP results in a global decrease in Mot1 binding. Using midpoint-versus-length mapping to assess the spatial relationship of Mot1 and TBP on chromatin, we find evidence that Mot1 approaches TBP from the upstream direction, consistent with its in vitro mode of action. Strikingly, inactivation of Mot1 leads to both increases and decreases in TBP-genome association. Sites of TBP gain tend to contain robust TATA boxes, while sites of TBP loss contain poly(dA:dT) tracts that may contribute to nucleosome exclusion. We propose that the action of Mot1 is required to clear TBP from intrinsically preferred (TATA-containing) binding sites, ensuring sufficient soluble TBP to bind intrinsically disfavored (TATA-less) sites. We have analyzed the genomic distributions of yeast TBP and Mot1 using Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin and sequencing (ORGANIC-seq).
2013-10-21 | E-GEOD-44200 | biostudies-arrayexpress
Project description:In eukaryotes, gene expression is performed by three RNA polymerases that are targeted to promoters by molecular complexes. A unique common factor, the TATA-box binding protein (TBP), is thought to serve as a platform to assemble pre-initiation complexes competent for transcription. Herein, we describe a novel molecular mechanism of nutrient regulation of gene transcription by dynamic O-GlcNAcylation of TBP. We show that O-GlcNAcylation at T114 of TBP blocks its interaction with BTAF1, hence the formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. Transcriptomic and metabolomic analyses of TBPT114A CRISPR/Cas9 edited cells showed that loss of O-GlcNAcylation at T114 increases TBP binding to BTAF1 and directly impacts expression of 408 genes. Lack of O-GlcNAcylation at T114 is associated with a striking reprograming of cellular metabolism induced by a profound modification of the transcriptome, leading to gross alterations in lipid storage.
2020-04-14 | GSE130309 | GEO