Transcriptional cofactors display core promoter class-specificity
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ABSTRACT:
PROVIDER: PRJNA477764 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| SRR7419420_1.fastq.gz | Fastqsanger.gz | |||
| SRR7419420_2.fastq.gz | Fastqsanger.gz | |||
| SRR7419430_1.fastq.gz | Fastqsanger.gz | |||
| SRR7419430_2.fastq.gz | Fastqsanger.gz | |||
| SRR7419440_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional cofactors display core promoter class-specificity in human
| PRJNA521352 | ENA
Project description:Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – CP preferences requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 23 different individually tethered Drosophila melanogaster COFs could activate transcription from any of 72,000 CP candidates in S2 cells. We selected COFs that represent different functional classes and enzymatic activities: histone-acetyl transferases (Nejire - the fly ortholog of CBP/P300, Mof, Gcn5 - ortholog of pCAF, Atac2, Tip60, Br140), three components of the COMPASS-like histone H3K4 methyltransferase complexes (Lpt, Trr and Trx), nucleosome remodeling ATP-ase (Brm), two Chromo or Chromo-shadow domain (Chro and Mof) and three Bromodomain (Brd8, Brd9 and fs(1)h - ortholog of Brd4) -containing COFs, three subunits of the Mediator Complex (MED15, MED24 and MED25), three subunits of the TFIID general transcription factor (Taf4, Tbp and Trf2) and three less well-characterized COFs (EMSY, Gfzf and Pzg). We used the strong transcriptional activator P65 as a positive and GFP as a negative control. In addition, we tested 6 COFs and the 2 controls in two other Drosophila cell lines: ovarian somatic cells (OSC) and Kc167 cells. We uncovered five classes of core promoters, distinguished by their differential response to specific cofactors and by the presence of known sequence elements, such as the TATA-box, Down-stream Promoter Element, or TCT motif. Moreover, the five promoter types show distinct chromatin properties at endogenous loci. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes, alternative promoters within the same genes, or even distinct transcription starting sites within the same promoters. Thus, cofactor–promoter compatibilities may underlie distinct transcriptional programs.
2019-05-15 | GSE116197 | GEO
Project description:Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – core promoter (CP) compatibilities requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 5 different individually tethered human COFs (MED15, BRD4, EP300, MLL3 and EMSY) activate transcription from a selection of 12,000 candidate sequences encompassing different types of gene core promoters, enhancers and control sequences. In addition, we used the strong transcriptional activator P65 as a positive control and GFP as a negative control. We found that different COFs preferentially activate different CPs. For instance, MED15 prefers TATA-box containing CPs, while MLL3 preferentially activates CpG island promoters. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes or alternative promoters within the same gene, and may underlie distinct transcriptional programs in human cells.
2019-05-15 | GSE126221 | GEO
Project description:Three general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UAS), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that few UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. We find that MED Tail and SAGA are dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter.
2023-03-17 | GSE217227 | GEO
Project description:Three general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UAS), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that few UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. We find that MED Tail and SAGA are dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter.
2023-03-17 | GSE227006 | GEO
Project description:Three general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UAS), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that few UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. We find that MED Tail and SAGA are dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter.
2023-03-17 | GSE217229 | GEO
Project description:Regulation of specific target genes by transcription factors is central to gene network control in development. How target specificity is achieved in eukaryotic genomes is poorly understood, as exemplified by the Hox family, which show limited in vitro DNA-binding specificity but clear functional specificity in vivo. We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. Ubx and Abd-A bind to similar target sites in accessible chromatin whereas Abd-B binds additional specific targets. Provision of the TALE class cofactors, Exd and Hth, alters the Ubx binding profile, enabling binding to additional targets in the genome. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in relatively DNase1 inaccessible chromatin, suggesting that competition with nucleosomes is a key factor determining Hox protein target specificity.
2015-12-07 | GSE69796 | GEO
Project description:Transcriptional cofactors (COFs) communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression1. Although some COFs have been shown to prefer certain promoter types2-5 over others (for example, see refs 6,7), the extent to which different COFs display intrinsic specificities for distinct promoters is unclear. Here we use a high-throughput promoter-activity assay in Drosophila melanogaster S2 cells to screen 23 COFs for their ability to activate 72,000 candidate core promoters (CPs). We observe differential activation of CPs, indicating distinct regulatory preferences or 'compatibilities'8,9 between COFs and specific types of CPs. These functionally distinct CP types are differentially enriched for known sequence elements2,4, such as the TATA box, downstream promoter element (DPE) or TCT motif, and display distinct chromatin properties at endogenous loci. Notably, the CP types differ in their relative abundance of H3K4me3 and H3K4me1 marks (see also refs 10-12), suggesting that these histone modifications might distinguish trans-regulatory factors rather than promoter- versus enhancer-type cis-regulatory elements. We confirm the existence of distinct COF-CP compatibilities in two additional Drosophila cell lines and in human cells, for which we find COFs that prefer TATA-box or CpG-island promoters, respectively. Distinct compatibilities between COFs and promoters can explain how different enhancers specifically activate distinct sets of genes9, alternative promoters within the same genes, and distinct transcription start sites within the same promoter13. Thus, COF-promoter compatibilities may underlie distinct transcriptional programs in species as divergent as flies and humans.
| S-EPMC7613045 | biostudies-literature
Project description:Regulation of specific target genes by transcription factors is central to gene network control in development. How target specificity is achieved in eukaryotic genomes is poorly understood, as exemplified by the Hox family, which show limited in vitro DNA-binding specificity but clear functional specificity in vivo. We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. Ubx and Abd-A bind to similar target sites in accessible chromatin whereas Abd-B binds additional specific targets. Provision of the TALE class cofactors, Exd and Hth, alters the Ubx binding profile, enabling binding to additional targets in the genome. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in relatively DNase1 inaccessible chromatin, suggesting that competition with nucleosomes is a key factor determining Hox protein target specificity. This ChIP-Seq study performed on Kc167 cells involves two experiments and 6 ChIP samples. In Experiment 1, we generated genome-wide binding profiles for Ubx, Abd-A and Abd-B. An equal volume of input chromatin was retained from each of the Hox samples and combined to represent the input, which was purified alongside the ChIP samples. We performed two biological replicates for each sample. Sequencing was performed using the Illumina MiSeq platform. In Experiment 2, we generated genome-wide binding profiles for Ubx, mutant Ubx and Ubx in the presence of Hth. We performed two biological replicates for each sample except Ubx where we performed just one. Sequencing was performed using the Illumina HiSeq 2000 platform. For all samples, Experiment 1 input chromatin was used as the reference control to assay ChIP enrichment.
2015-12-07 | E-GEOD-69796 | biostudies-arrayexpress
Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters M-bM-^@M-^S one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genesM-bM-^@M-^Y core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.
2014-12-10 | E-GEOD-57876 | biostudies-arrayexpress