 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 04, 2021 |
| Title |
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Circadian gene expression is essential for organisms to adjust cellular responses and anticipate daily changes in the environment. In addition to its physiological importance, the clock circuit represents an ideal, temporally resolved, system to study transcription regulation. Here, we analysed changes in spatial mouse liver chromatin conformation using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription in mouse liver. We found circadian topologically associated domains switched assignments to the transcriptionally active, open chromatin compartment and the inactive compartment at different hours of the day while their boundaries stably maintain their structure over time. Individual circadian gene promoters displayed maximal chromatin contacts at times of peak transcriptional output and the expression of circadian genes and contacted transcribed regulatory elements, or other circadian genes, was phase-coherent. Anchor sites of promoter chromatin loops were enriched in binding sites for liver nuclear receptors and transcription factors, some exclusively present in either rhythmic or stable contacts. The circadian 3D chromatin maps provided here identify the scales of chromatin conformation that parallel oscillatory gene expression and protein factors specifically associated with circadian or stable chromatin configurations.
|
| |
|
| Overall design |
Total stranded RNAseq on mouse liver samples at four timepoints (ZT0, 6, 12, 18) during a circadian cycle. ZT0=lights on, ZT12=lights off
|
| |
|
| Contributor(s) |
Furlan-Magaril M, Ando-Kuri M, Arzate-Mejia R, Morg J, Cairns J, Poot-Hernandez CA, Andrews S, Varnai C, Virk B, Wingett SW, Fraser P |
| Citation(s) |
34099014 |
| |
| Submission date |
Jul 27, 2020 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
mfurlan@ifc.unam.mx
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (16)
|
|
| This SubSeries is part of SuperSeries: |
| GSE155161 |
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle |
|
| Relations |
| BioProject |
PRJNA648875 |
| SRA |
SRP273701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155160_RNAseq_ZT0_merge_norm_forward.bw |
27.0 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT0_merge_norm_reverse.bw |
24.1 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT12_merge_norm_forward.bw |
28.5 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT12_merge_norm_reverse.bw |
25.7 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT18_merge_norm_forward.bw |
25.9 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT18_merge_norm_reverse.bw |
23.1 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT6_merge_norm_forward.bw |
29.6 Mb |
(ftp)(http) |
BW |
| GSE155160_RNAseq_ZT6_merge_norm_reverse.bw |
26.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...