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Series GSE43070 Query DataSets for GSE43070
Status Public on Oct 20, 2013
Title Genome-wide Analysis of Chromatin Interactions in Human Cells
Organism Homo sapiens
Experiment type Other
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Millions of cis-regulatory sequences have recently been found in the human genome, but the function of most cis-elements are not yet clear, in part due to the difficulty in determining their regulatory targets, which are often located millions of base pairs away and separated by one or more unrelated genes. To address this problem, the Hi-C method has been developed to identify long-range looping interactions in a genome-wide, unbiased fashion. However, current data analysis of Hi-C datasets cannot fully resolve regulatory interactions between enhancers and promoters due to the low resolution. Here, we generated a high-depth Hi-C dataset and applied a new analysis method that offers improved resolution permitting genome-wide identification of nearly one million chromatin interactions. We demonstrated the use of Hi-C to identify target promoters of enhancers regulated by NF-κB signaling and signal-dependent dynamic chromatin interaction at these enhancers in human cells. Surprisingly, our results showed that most NF-κB binding sites are looped to their regulatory targets prior to activation of the signaling pathway, and appear to undergo little change during signaling. This observation suggests that the chromatin organization landscape, once established in a cell type, is rather stable and may influence the selection and activation of target genes by a transcription factor.
 
Overall design We performed Hi-C analysis using a human fibroblast cell line IMR90 before and after NF-κB activation. In the meantime, we also performed ChIP-seq experiments to map the location of NF-κB p65 subunit, RNA polymerase II, p300, and several histone modifications (including H3K4me1, H3K4me3, H3K27ac and H3K36me3) in IMR90 cells before and after transient TNF-α stimulation. Additionally, to monitor the dynamic transcription profiles, we also performed Global Run-On sequencing (GRO-seq).
 
Contributor(s) Jin F, Li Y, Ren B
Citation(s) 24141950
Submission date Dec 20, 2012
Last update date May 15, 2019
Contact name Fulai Jin
E-mail(s) fxj45@case.edu
Phone 2163681811
Organization name Case Western Reserve University
Lab Fulai Jin
Street address 10900 Euclid Avenue
City Cleveland
State/province OH - OHIO
ZIP/Postal code 44106
Country USA
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (53)
GSM1055800 Hi-C IMR90 replicate 1
GSM1055801 Hi-C IMR90 replicate 2
GSM1055802 Hi-C IMR90_TNF-α replicate 1
Relations
BioProject PRJNA184350
SRA SRP017631

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
GSE43070_RAW.tar 76.7 Gb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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