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Comparative ChIP-chip analysis of general transcription factor TFIIB and negative cofactor NC2 in human B cells

ABSTRACT: A comparative ChIP-chip analysis of TFIIB and NC2 in human B cells reveals that basal core promoter architectures control the equilibrium between NC2 and preinitiation complexes. We conducted a comparative ChIP-chip and gene expression analysis of TFIIB in human B cells and analyze associated core promoter architectures. TFIIB occupancy relates well to gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA consensus and TATA-like motifs but not the previously in vitro defined TFIIB recognition elements (BREs) are enriched in approximately 5% of the genes. Further insight was obtained by performing a parallel ChIP-chip analysis of the TFIIB antagonist NC2. The latter identifies a highly related target gene set. Nonetheless, subpopulations show strong variations in TFIIB/NC2 ratios, with high NC2/TFIIB ratios correlating to promoters that show dispersed transcription start site patterns and lacking defined core elements. Conversely, high TFIIB/NC2 ratios select for conserved core promoter elements that include TATA and INR (initiator), the upstream TFIIB recognition element (BREu) and the downstream promoter element (DPE).

ORGANISM(S): Homo sapiens

PROVIDER: GSE19562 | GEO | 2009/12/19

SECONDARY ACCESSION(S): PRJNA122407

REPOSITORIES: GEO

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Comparative ChIP-chip analysis of general transcription factor TFIIB and negative cofactor NC2 in human B cells

Project description:A comparative ChIP-chip analysis of TFIIB and NC2 in human B cells reveals that basal core promoter architectures control the equilibrium between NC2 and preinitiation complexes. We conducted a comparative ChIP-chip and gene expression analysis of TFIIB in human B cells and analyze associated core promoter architectures. TFIIB occupancy relates well to gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA consensus and TATA-like motifs but not the previously in vitro defined TFIIB recognition elements (BREs) are enriched in approximately 5% of the genes. Further insight was obtained by performing a parallel ChIP-chip analysis of the TFIIB antagonist NC2. The latter identifies a highly related target gene set. Nonetheless, subpopulations show strong variations in TFIIB/NC2 ratios, with high NC2/TFIIB ratios correlating to promoters that show dispersed transcription start site patterns and lacking defined core elements. Conversely, high TFIIB/NC2 ratios select for conserved core promoter elements that include TATA and INR (initiator), the upstream TFIIB recognition element (BREu) and the downstream promoter element (DPE). Two biological samples from LCL 721 lymphoblastoid human B cells were subjected to ChIP-chip analysis of TFIIB and NC2 using a Nimblegen human promoter array (based on the HG17 genome build) covering 1.5 kb DNA around transcription start sites.

2010-05-16 | E-GEOD-19562 | biostudies-arrayexpress

Identification of the human DPR core promoter element using machine learning

Project description:The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription, but the downstream core promoter in humans has been difficult to understand. Here we analyse the human Pol II core promoter and use machine learning to generate predictive models for the downstream core promoter region (DPR) and the TATA box. We developed a method termed HARPE (high-throughput analysis of randomized promoter elements) to create hundreds of thousands of DPR (or TATA box) variants, each with known transcriptional strength. We then analysed the HARPE data by support vector regression (SVR) to provide comprehensive models for the sequence motifs, and found that the SVR-based approach is more effective than a consensus-based method for predicting transcriptional activity. These results show that the DPR is a functionally important core promoter element that is widely used in human promoters. Notably, there appears to be a duality between the DPR and the TATA box, as many promoters contain one or the other element. More broadly, these findings show that functional DNA motifs can be identified by machine learning analysis of a comprehensive set of sequence variants.

2020-06-04 | GSE139635 | GEO

Characterization of the TCT motif reveals a crucial role of the core promoter micro-environment in gene regulation

Project description:The signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversityThe signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversity in core promoter motif poises their composition as a means to regulate gene expression. We utilized genome-wide (5’GRO-seq) and biochemical methods to characterize the TCT motif in humans and Drosophila and show that it is a functionally conserved RNA polymerase II core promoter element. Human TCT-containing promoters are ~3-fold enriched for the TATA box motif while Drosophila promoters are depleted. The downstream core promoter element (DPE) is underrepresented. Combinatorial analysis revealed the TCT motif to cooperatively facilitate transcription with the TATA box in some instances, but not others implying a role for the core promoter micro-environment in gene regulation. The interaction among core promoter elements is therefore not as straightforward as previously thought. TCT-containing promoters predominantly regulate the expression of genes involved in translation, thereby providing an example how core promoter motifs facilitate regulatory specialization. This may explain why diverse translation-related genes are observed as commonly altered in some cancers.

2017-01-01 | GSE68677 | GEO

Structural basis of SNAPc-dependent snRNA transcription intiation by RNA polymerase II

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

Requirements for preinitiation complex formation in vivo

Project description:Transcription by RNA polymerase (Pol) II requires assembly of a preinitiation complex (PIC) composed of general transcription factors (GTFs) bound at the core promoter. In vitro, the TATA-binding protein (TBP), TFIIB, TFIIF, and Pol II are essential for PIC formation and transcriptional initiation, whereas TFIIA, TFIIE, and TFIIH are not required under certain conditions. In addition, the PIC is stable in the absence of nucleotide triphosphates, and sequential addition of GTFs results in a series of partial PICs. Here, we analyze the roles of all GTFs in yeast cells by measuring PIC formation and Pol II transcription upon depletion of individual GTFs. All GTFs are essential for TBP binding and Pol II transcription in vivo, suggesting that partial PICs composed of GTF subsets do not exist at appreciable levels. In contrast, TBP-associated factors (TAFs) contribute to Pol II transcriptional activity at most (and perhaps all) genes, but TAF-independent transcription occurs at a substantial level, particularly at promoters lacking canonical TATA elements. Lastly, unlike the case in vitro, PICs are not observed in cells deprived of uracil, and presumably UTP, suggesting a mechanism that removes transcriptionally inactive PICs from promoters.

2019-02-27 | GSE122734 | GEO

Pol II (Rpb3) ChIP-seq in Drosophila melanogaster S2 cells

Project description:Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoters in metazoans implies that steps other than Pol II recruitment are rate-limiting and regulated 1-6. By integrating genome-wide Pol II chromatin immunoprecipition (ChIP) and Global Run-On (GRO) genomic data sets from Drosophila cells, we examined critical features of Pol II near promoters. The accumulation of promoter-proximal polymerase is widespread, occurring on 70% of active genes; and unlike elongating Pol II within the body of genes, promoter Pol II are held paused by factors like NELF, unable to transcribe unless nuclei are treated with strong detergent. Notably, we find that the vast majority of promoter-proximal Pol II detected by ChIP are paused, thereby identifying the biochemical nature of this rate-limiting step in transcription. Finally, we demonstrate that Drosophila promoters do not have the upstream divergent Pol II that is seen so broadly and prominently on mammalian promoters. We postulate this is a consequence of Drosophila’s extensive use of directional core promoter sequence elements, which contrasts with mammals’ lack of directional elements and prevalence of CpG island core promoters. In support of this idea, we show that the fraction of mammalian promoters containing a TATA box core element is dramatically depleted of upstream divergent transcription. ChIP-seq data set for Pol II (rpb3) (2 replicates).

2012-10-25 | E-GEOD-23542 | biostudies-arrayexpress

Transcriptional start site mapping of P14 WT and P14 Tbpl2-/- mutant mouse oocytes

Project description:We used SLIC-CAGE to map transcriptional start sites (TSSs) of P14 WT and P14 Tbpl2-/- mutant mouse oocytes. Comparison of WT and Tbpl2-/- oocytes demonstrates that Tbpl2 guides transcriptional start site selection in the growing oocyte. This TSS selection is different compared to the canonical somatic type of TSS selection and depends on TATA-like elements as core promoter motifs, recognised by Tbpl2.

2020-11-12 | E-MTAB-8866 | biostudies-arrayexpress

A TATA binding protein regulatory network

Project description:Background: Eukaryotic genes are controlled by proteins that assemble stepwise into a transcription complex. How the individual biochemically-defined assembly steps are coordinated and applied throughout a genome is largely unknown. Here, we model and experimentally test a portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome. Results: Biochemical knowledge is used to formulate a series of coupled TBP regulatory reactions involving TFIID, SAGA, NC2, Mot1, and promoter DNA. The reactions are then linked to basic segments of the transcription cycle and modeled computationally. A single framework is employed, allowing the contribution of specific steps to vary from gene to gene. Promoter binding and transcriptional output are measured genome-wide using ChIP-chip and expression microarray assays. Mutagenesis is used to test the framework by shutting down specific parts of the network. Conclusion: The model accounts for the regulation of TBP at most transcriptionally active promoters and provides a conceptual tool for interpreting genome-wide data sets. The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale. Keywords: genetic mutation analysis

2007-04-01 | GSE7385 | GEO

MOT1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Project description:An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

2016-11-11 | GSE81480 | GEO

HSF1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

2016-11-11 | GSE81479 | GEO

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