Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA491668 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7868840.fastq.gz	Fastqsanger.gz
	SRR7868850.fastq.gz	Fastqsanger.gz
	SRR7868860.fastq.gz	Fastqsanger.gz
	SRR7868870.fastq.gz	Fastqsanger.gz
	SRR7868880.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 220

Similar Datasets

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 [GRO-Seq]

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

| PRJNA491665 | 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.

| S-EPMC6760001 | biostudies-literature

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

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

2019-06-27 | GSE120110 | GEO

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

DEAD box RNA helicases are pervasive protein kinase interactors and activators

Project description:DEAD box (DDX) RNA helicases are a large family of ATPases, many of which have unknown functions. There is emerging evidence that besides their role in RNA biology, DDX proteins may stimulate protein kinases. To investigate if protein kinase-DDX interaction is a more widespread phenomenon, we conducted three orthogonal large-scale screens, including proteomics analysis with 32 RNA helicases, protein array profiling, and kinome-wide in vitro kinase assays. We retrieved Ser/Thr protein kinases as prominent interactors of RNA helicases and report hundreds of binary interactions. We extracted members of eleven protein kinase families, which bind to - and are stimulated by - DDX proteins, including CAMK, CDK, CK1, CK2, DYRK, MARK, NEK, PRKC, SPRK, STE7/MAP2K, and STE20/PAK family members. We identified MARK1 in all screens and validated that DDX proteins accelerate MARK1 catalytic rate. The findings indicate pervasive interactions between protein kinases and DEAD box RNA helicases and provide a rich resource to explore their regulatory relationships.

2024-03-10 | PXD043289 | Pride

Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells

Project description:Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells

| PRJNA628878 | ENA