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Series GSE120104 Query DataSets for GSE120104
Status Public on Jun 27, 2019
Title Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design Examination of RBP ChIP-seq with 2 replicated experiments in HepG2 and K562 cells
 
Contributor(s) Xiao R, Chen J, Fu X
Citation(s) 31251911
Submission date Sep 18, 2018
Last update date Sep 26, 2019
Contact name Rui Xiao
E-mail(s) xiaorui9@whu.edu.cn
Organization name Wuhan University
Department Medical Research Institute
Lab RNA Biology Lab
Street address Medical Research Institute, Wuhan University
City Wuhan
State/province Hubei
ZIP/Postal code 430071
Country China
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (110)
GSM3393527 SRSF1_ChIP-seq_HepG2
GSM3393528 SRSF3_ChIP-seq_HepG2
GSM3393529 SRSF4_ChIP-seq_HepG2
This SubSeries is part of SuperSeries:
GSE120110 Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription
Relations
BioProject PRJNA491668
SRA SRP162019

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120104_RAW.tar 64.2 Gb (http)(custom) TAR (of BW, NARROWPEAK)
GSE120104_RBM25chip-NC-OPTIMAL_ppr.IDR0.02.filt.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
GSE120104_YY1chip-NC-OPTIMAL_ppr.IDR0.02.filt.narrowPeak.gz 805.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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