Ontology highlight
ABSTRACT:
PROVIDER: PRJNA257920 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1542280.fastq.gz | Fastqsanger.gz | |||
| SRR1542290.fastq.gz | Fastqsanger.gz | |||
| SRR1542300.fastq.gz | Fastqsanger.gz | |||
| SRR1542310.fastq.gz | Fastqsanger.gz | |||
| SRR1542320.fastq.gz | Fastqsanger.gz |
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Project description:Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (ChIP-seq)
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Project description:Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (Gro-seq)
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Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Chromatin Immunoprecipitation (ChIP) assay followed by high throughput sequencing (ChIP-seq)
2014-10-09 | E-GEOD-60270 | biostudies-arrayexpress
Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq)
2014-10-09 | E-GEOD-60271 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Refer to individual Series
2014-10-09 | E-GEOD-60272 | biostudies-arrayexpress
Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.
2014-10-09 | GSE60270 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.
2014-10-09 | GSE60272 | GEO
Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.
2014-10-09 | GSE60271 | GEO
Project description:The enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. CEeRNA regulates transcription of the adjacent MyoD gene while DRReRNA affects expression of Myogenin in trans. We found that DRReRNA is recruited at the Myogenin locus where it colocalizes with Myogenin nascent transcripts. DRReRNA associates with the Cohesin complex and such association correlates with its transactivating properties. Despite being expressed in undifferentiated cells, Cohesin is not loaded on Myogenin until the cells start expressing DRReRNA, which is then required for Cohesin chromatin recruitment and maintenance. Functionally, depletion of either Cohesin or DRReRNA reduces chromatin accessibility, prevents Myogenin activation, and hinders muscle cell differentiation. Thus, DRReRNA ensures spatially appropriate Cohesin loading in trans to regulate gene expression.
2018-06-01 | GSE113248 | GEO
Project description:Estrogen receptors alpha (ERα) converges estrogen signaling by orchestrating estrogen (E2)-dependent transcription regulation. Upon binding to the chromatin, ERα serves as a nucleation site for de novo formation of transcription enhancer complexes. Steroid receptor coactivators family proteins (SRCs, a.k.a p160) and Mediator complex are the two coregulators for ERα that directly interact with the receptors and control enhancer activity by regulating recruitment of other coregulators and transcription machinery. Lysine acetyltransferase p300/CBP is also a critical coregulator for ERα that is recruited through SRCs in stable ERα enhancer complex. ERα enhancers exhibit common enhancer features including enrichment of enhancer-specific histone modification (e.g. H3K4me1 and H3K27ac), coregulator recruitment, and active transcription. Despite of recognition of those enhancer characteristics, the order of assembly and functions and the functional relationships among enhancer features during active enhancer complex formation is not well understood. Using the time course genomics and molecular biology assays, we dissect the order of assembly and functions of ERα enhancer complex formation. We describe the mechanism of SRC-independent p300 recruitment mediated by Mediator, leading to initial partial activation of the ERα enhancer for enhance priming. Maturation of the enhancer in turn switches the p300 recruitment mechanism to an SRC-dependent manner, resulting in the maximum enhancer activity and transcription outcomes. Thus, our results illustrate the role of SRC in enhancing the activity of primed enhancers. Furthermore, we show that forced recruitment of p300 to inactive enhancers establishes active enhancer marks and induces ERα-target gene expression. Together, we demonstrate the molecular mechanisms of ERα enhancer complex formation where p300 plays a pivotal role in enhancer activation and target gene expression controlled by distinctive mechanisms through different stages of ERα enhancer complex formation.
2018-05-21 | GSE95121 | GEO