ChIP-Seq of TBP in Mouse Embryonic Stem Cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE22303 | GEO | 2010/06/15
SECONDARY ACCESSION(S): PRJNA127397
REPOSITORIES: GEO
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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.
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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: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.
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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.
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Project description:During mitosis, TATA-binding protein(TBP), which remains bound to DNA during mitosis, recruits PP2A and also interacts with a subunit of the condensin complex to allow efficient dephosphorylation and inactivation of condensin near these promoters to inhibit their compaction. These result suggest that TBP function is not only important for expression of genes transcribed bDuring mitosis, TATA-binding protein(TBP), which remains bound to DNA during mitosis, recruits PP2A and also interacts with a subunit of the condensin complex to allow efficient dephosphorylation and inactivation of condensin near these promoters to inhibit their compaction. These result suggest that TBP function is not only important for expression of genes transcribed by all three RNA polymerase during interphase, but also for transmitting the memory of gene activity through mitosis to daughter cellsy all three RNA polymerase during interphase, but also for transmitting the memory of gene activity through mitosis to daughter cells We use ChIP-chip approach to identify TBP-bindind sites in mitotic Jurkat cells at genome-wide level. Input DNA fragments and DNA fragments immunoprecipitated by TBP antibodies by ChIP assay on mitotic Jurkat cells were used to probe the Affymetrix Genechip human tiling 2.0c to identift TBP-binding sites in mitotic Jurkat cells. Input and ChIP sample were replicated three times as following: Input rep1, TBP ChIP1, Input rep2, TBP ChIP2, Input rep3, TBP ChIP3.
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Project description:TAF4 directed immunoprecipitation of the the Pre-initiation complex from mouse embryonic stem cells with or without depletion of TATA-box binding protein (TBP).
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Project description:Genome/chromosome organization is highly ordered and controls nuclear events. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosome organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation.
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Project description:The study was carried out to identify changes in expression of microRNAs in Neuro2A cells transfected with TATA binding protein (TBP) containing a polyglutamine expansion (59 glutamine-59Q) compared to normal TBP.
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