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Series GSE68831 Query DataSets for GSE68831
Status Public on Apr 04, 2016
Title Long-range chromosome interactions mediated by cohesin shape circadian gene expression [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. We analyzed the interactome of a Bmal1-bound enhancer upstream of a clock gene, Nr1d1, by 4C-seq and observed that cohesin binding sites are enriched in the interactome. Integrating circadian transcriptome data and cistrome data, we found that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites facilitate the interaction between circadian enhancer and promoter. A coarse-grained model integrating the long-range effect of cohesin and CTCF markedly improved our mechanistic understanding of circadian gene expression. This model is subsequently supported by our RNA-seq data from cohesin knockout cells. Cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. Taken together, our study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.
 
Overall design RNA-Seq in WT and Smc3-/- mouse embryonic fibroblast cells
 
Contributor(s) Xu Y, Guo W, Li P, Zhang Y, Fan Z, Zhao Z, Yan J
Citation(s) 27135601
Submission date May 13, 2015
Last update date May 15, 2019
Contact name Yichi Xu
E-mail(s) xuy2@mskcc.org
Organization name MSKCC
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1682610 wt20_RNA-Seq
GSM1682611 wt32_RNA-Seq
GSM1682612 ko20_RNA-Seq
This SubSeries is part of SuperSeries:
GSE68832 Long-range chromosome interactions mediated by cohesin shape circadian gene expression
Relations
BioProject PRJNA283889
SRA SRP058292

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
GSE68831_RAW.tar 380.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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