RNA Polymerase II transcription independent of TBP [NET-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA851782 | ENA |
REPOSITORIES: ENA
Similar Datasets
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 transcription independent of TBP
| PRJNA723216 | ENA
Project description:RNA Polymerase II transcription independent of TBP (CUT&Tag)
| PRJNA851783 | ENA
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: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:The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. To better map transcription genome-wide at base pair resolution and with transcription/elongation factor dependency we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). NET-prism introduces an immunoprecipitation to capture RNA Pol II – associated proteins, which reveals the interaction of these proteins with active RNA Pol II. Application of NET-prism on different Pol II variants (Pol II S2ph, Pol II S5ph), elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals diverse Pol II signals, at a single nucleotide resolution, with regards to directionality and intensity over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity.
2019-07-02 | GSE107257 | GEO
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
Project description:Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB, and XPB.
| PRJNA799326 | ENA
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:RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [NET-seq]
| PRJNA885861 | ENA