 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 27, 2021 |
| Title |
Chromatin states and genomic organization impact local replication features and timing [Repli-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Replication timing (RT) control is linked to histone modifications (HMs) and genome architecture. However, HM landscape across cell cycle and its relationship with RT and chromatin modifiers have not been comprehensively assessed. Here we perform detailed replication profiling together with cell cycle profiling of multiple HMs, ATAC-seq, and gene expression. We classify 97% of the genome into four gross chromatin states, including a previously uncharacterized intergenic H3K36me2 state. RT and associated replication features (e.g. initiation zones) quantitatively associate with these chromatin states, HM dynamics, and spatial chromatin structure. Furthermore, overexpression of the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT across 12% of the genome. RT regulation is strongly linked to KDM4A-associated HMs and enhancer-like elements. Lastly, replication within the intergenic H3K36me2 neighborhoods is sensitive to KDM4A overexpression and is controlled as wide megabase-scale units. In conclusion, these studies establish a critical role for chromatin regulation in directing RT genome-wide.
|
| |
|
| Overall design |
Examination of replication timing in a replicate of RPE control or stably overexpressing KDM4A, at seven phases of cell cycle: ES, LS, G2/M, S1, S2, S3, S4
|
| |
|
| Contributor(s) |
Whetstine J, Sadreyev R, Ji F, van Rechem C |
| Citation(s) |
34610305 |
| |
| Submission date |
May 28, 2021 |
| Last update date |
Oct 27, 2021 |
| Contact name |
Fei Ji |
| Organization name |
Massachusetts General Hospital
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (28)
|
|
| This SubSeries is part of SuperSeries: |
| GSE175752 |
Chromatin states and genomic organization impact local replication features and timing |
|
| Relations |
| BioProject |
PRJNA733486 |
| SRA |
SRP321792 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE175751_RAW.tar |
16.4 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...