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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]

ABSTRACT: Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]

PROVIDER: PRJNA491665 | ENA |

REPOSITORIES: ENA

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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription

Project description:Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription

| PRJNA491670 | ENA

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]

Project description:Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]

| PRJNA491667 | ENA

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]

Project description:Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]

| PRJNA491668 | ENA

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]

Project description:Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription. As part of the ENCODE consortium, we embarked on a large-scale RBP ChIP-seq analysis, revealing broad presence of RBPs in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show great preference for hotspots in the genome, particularly gene promoters, where their binding is frequently linked to transcriptional output. Self-organizing map reveals extensive co-binding events between TFs and RBPs, as exemplified by those between YY1, a known RNA-dependent TF, and RBM25, an RBP involved in alternative splicing. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may bridge specific TF-RNA interactions to control transcription.

2019-06-27 | GSE120105 | GEO

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

| S-EPMC6760001 | biostudies-literature

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]

2019-06-27 | GSE120104 | GEO

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]

2019-06-27 | GSE120023 | GEO

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-27 | GSE120110 | GEO

Genome-wide identification of RNA-chromatin interactions in Arabidopsis [GRO-seq]

Project description:Genome-wide identification of RNA-chromatin interactions in Arabidopsis [GRO-seq]

| PRJNA752623 | ENA

GRO-seq in human CD34+ erythrocytes

Project description:Purpose: GRO-seq is a robust method to examine the nascent RNA transcriptome in the genome level Methods: The GRO-seq measures the trancription of nascent RNAs in the genome. From human CD34+ erythrocytes treated with veichle or T4 we conducted GRO-seq to examine the transcripome.

2017-09-06 | GSE102819 | GEO

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