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| Status |
Public on Apr 04, 2016 |
| Title |
Long-range chromosome interactions mediated by cohesin shape circadian gene expression [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy 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.
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|
| Overall design |
Bmal1 ChIP-Seq in WT mouse embryonic fibroblast cells
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| |
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| Contributor(s) |
Xu Y, Guo W, Li P, Zhang Y, Fan Z, Zhao Z, Yan J |
| Citation(s) |
27135601 |
| |
| Submission date |
Jan 25, 2016 |
| 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) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE68832 |
Long-range chromosome interactions mediated by cohesin shape circadian gene expression |
|
| Relations |
| BioProject |
PRJNA309640 |
| SRA |
SRP068827 |
