RNA Polymerase II transcription independent of TBP
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ABSTRACT:
PROVIDER: PRJNA723216 | ENA |
REPOSITORIES: ENA
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Project description:RNA Polymerase II transcription independent of TBP [NET-seq]
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Project description:RNA Polymerase II transcription independent of TBP (CUT&Tag)
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Project description:Using CUT&Tag, a chromatin profiling technique, we show that TBP depletion via IAA surprisingly does not affect RNA Pol II transcription but affects RNA Pol III transcription. Additionally, induction of genes via heat shock and retinoic acid treatment does not require TBP. We also show that a metazoan specific paralog TRF2 does not compensate for TBP for RNA Pol II transcription and that the TFIID subunit of the Pre-initiation Complex can still form with specific subunits still binding onto DNA when TBP is depleted.
2023-04-12 | GSE206694 | GEO
Project description:Using NET-seq to profile nascent RNA transcription, we show that auxin-mediated depletion of TBP does not affect Pol II transcription and gene activation via heat shock.
2023-04-12 | GSE206695 | GEO
Project description:RNA Polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes such as small nuclear RNA (snRNA) genes is not understood at the structural level. Here we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol II preinitiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE) located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc called wing-1 and wing-2 bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.
2023-03-11 | PXD033638 | Pride
Project description:The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID nucleates RNA Polymerase II (Pol II) preinitiation complex formation on gene promoters and thus, is crucial for Pol II transcription. Germline knock out of several mouse TFIID subunits (Tbp, Taf7, Taf8, and Taf10) results in lethality at embryonic day 4.0, demonstrating the fundamental role of holo-TFIID in transcription. We identified a child harboring a splice-site mutation in TAF8, who has intellectual disability, poor growth, progressive spasticity and microcephaly. The c.781-G>A TAF8 mutation in this patient resulted in a frame shift, which affected the final 50 carboxy terminal amino acids of TAF8. We found that the mutant TAF8 protein is unstable and the patient c.781-G>A TAF8 primary fibroblasts did not form canonical TFIID complexes. Astonishingly however, genome-wide RNA pol II occupancy and pre-mRNA transcription on the tested genes was unaffected in the patient’s primary fibroblasts. This study indicates that perturbed TFIID function is less deleterious for transcription in human cells than originally anticipated.
2018-04-16 | PXD008084 | Pride
Project description:General transcription factors (GTFs) are required for RNA polymerase II (Pol II) to initiate transcription at promoters. In this study, we determined the effects of acute depletion of TBP, TAF1, TAF4, TFIIB, and XPB in HAP1 cells. We performed precision nuclear run-on sequencing (PRO-Seq) and quantified nascent transcripts arising from more than 70,000 promoters. The average dependencies for each factor across all promoters varied widely even though levels of depletions were similar. Many of the effects could be attributed to the presence or absence of core promoter elements. Depletion of TBP had a large effect on only a small fraction of Pol II and Pol III promoters. TFIIB depletion also led to readthrough transcription downstream of the 3′ ends of genes. We conclude that promoter activity is influenced by recruitment of TFIID, sequence-specific transcription factors, and interaction of the preinitiation complex (PIC) with the +1 nucleosome.
2022-07-17 | GSE194153 | GEO
Project description:RNA polymerase II (Pol II) transcription initiation starts with the assembly of the preinitiation complex (PIC) on core promoters. The PIC is composed of six general transcription factors (GTFs). The recognition of the core promoter sequences by the TFIID GTF complex is the first step of the PIC assembly. In metazoans, holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Genetic depletion of different murine TAFs have shown that TAFs such as TAF7 or TAF10, can be either required, or dispensable for Pol II transcription, depending on different cellular contexts. In this report, we depleted TAF7 and/or TAF10 in the same cellular system; either in mesodermal progenitors during mouse development or in mESCs. In these two models, TAF7 depletion leads to a milder phenotype compared to TAF10 depletion. As TAF10 is also a subunit of the transcriptional co-activator Spt-Ada-Gcn5 acetyl transferase (SAGA), we first showed that the difference in phenotype between the Taf7 and Taf10 mutant is not due to the SAGA effect, at least for mESCs. Immunoprecipitations coupled with mass spectrometry analyses from mESCs lysates assembly of holo-TFIID complex is rapidly affected after induction of the depletion. In line with the model of holo-TFIID sequential assembly, TAF10 depletion leads to an early defect with formation of the core-TFIID, while TAF7 depletion results in the formation of a TAF7-less TFIID. Thus, the difference in phenotype severity correlates with the degree of TFIID disassembly. Surprisingly, no major global changes in Pol II transcription could be observed after either TAF7 or TAF10 depletion. Our data suggest that the inducible loss of fully assembled canonical TFIID does not correlate with the lack of global Pol II transcription activity changes suggesting that partially assembled TFIID complexes can participate in Pol II transcription initiation, with only limited effect on Pol II nascent transcription.
2024-05-21 | PXD046459 | Pride
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 general transcription factor TFIID is composed of the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex containing TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depletion of TAFs that are present or ectopic expression of TAFs that are absent, results in misregulation of pluripotency gene expression and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew. ChIP-chip was used in this study to assess the global pattern of TAF recruitment at a gene promoters, to verify the existence of two classes of genes which differentially recruit and use TAF proteins for transcription initiation. Comparison of recruitment of 4 TAFs (TAF3, TAF5, TAF7 and TAf11) with the recruitment of TBP and RNA Polymerase II in wild-type H9 embryonic stem cells from replicate experiments
2012-11-19 | E-GEOD-39312 | biostudies-arrayexpress