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Series GSE175751 Query DataSets for GSE175751
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)
GSM5345582 RPE.Ctrl.ES.rep1
GSM5345583 RPE.Ctrl.LS.rep1
GSM5345584 RPE.Ctrl.G2.rep1
This SubSeries is part of SuperSeries:
GSE175752 Chromatin states and genomic organization impact local replication features and timing
Relations
BioProject PRJNA733486
SRA SRP321792

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE175751_RAW.tar 16.4 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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