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 [GRO-Seq]

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

PROVIDER: PRJNA491665 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7868790.fastq.gz	Fastqsanger.gz
	SRR7868800.fastq.gz	Fastqsanger.gz
	SRR7868810.fastq.gz	Fastqsanger.gz
	SRR7868820.fastq.gz	Fastqsanger.gz
	SRR7868791.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 38

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 [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

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

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

Project description: Not available

| S-EPMC6760001 | biostudies-literature

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

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

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites

Project description:We developed a general method based on RNA Antisense Purification (RAP) to identify the intermolecular RNA-RNA interactions of a target RNA (RAP-RNA). RAP-RNA identifies endogenous RNA-RNA complexes through in vivo crosslinking, RNA capture with antisense oligonucleotides, and high-throughput RNA sequencing. This approach provides a systematic view of other RNAs that interact with a target RNA, and furthermore can distinguish between direct and indirect RNA-RNA interactions through the use of crosslinking reagents with different reactivities with proteins and nucleic acids. We applied this method to numerous small and large noncoding RNAs, including U1 snRNA, Malat1 lncRNA, Xist lncRNA, U3 snoRNA, U17/Snora73a snoRNA and U12 snRNA. We examined the RNA and chromatin interactions of ncRNAs in mouse embryonic stem cells. We developed and applied three related protocols: RAP-RNA[AMT], RAP-RNA[FA], and RAP-RNA[FA-DSG]. In the RAP-RNA[AMT] protocol, we fixed direct RNA-RNA hybrids in mouse embryonic stem (ES) cells with 4'-aminomethyltrioxalen (AMT), a psoralen-derivative crosslinker; AMT generates inter-strand crosslinks between uridine bases in RNA but does not react with proteins. In the RAP-RNA[FA] protocol, we used a different crosslinking strategy to capture both direct and indirect RNA-RNA interactions: we fixed ES cells using formaldehyde (FA), which crosslinks protein-RNA and protein-protein interactions and thus can capture both indirect interactions as well as direct interactions that are caged or flanked by proteins. In the RAP-RNA[FA-DSG] protocol, we fixed with both FA and disuccinimidyl glutarate (DSG), a strong protein-protein crosslinker, to more efficiently capture RNAs linked indirectly through multiple protein intermediates.

2014-09-01 | E-GEOD-55914 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data