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Series GSE80391 Query DataSets for GSE80391
Status Public on May 11, 2016
Title Epigenetic features of differentiation-regulated replication origins
Organism Homo sapiens
Experiment type Other
Summary To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role for chromatin in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNAse hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 50,000 regions that actively initiated replication in all cell types examined and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group consisted of origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type specific origins preferentially replicated during late S-phase.
Overall design Nascent strands were purified with the lambda exonuclease methods from normal and cancer cells and sequenced.
Contributor(s) Aladjem MI
Citation(s) 27168766, 27924004
Submission date Apr 18, 2016
Last update date May 15, 2019
Contact name Christophe E Redon
Phone 240-760-7338
Organization name NIH
Street address 37 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (8)
GSM2125829 Nascent strands reads from U2OS_rep1
GSM2125830 Nascent strands reads from U2OS_rep2
GSM2125831 Control Reads (random shear) from U2OS
BioProject PRJNA318786
SRA SRP073451

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Supplementary file Size Download File type/resource
GSE80391_RAW.tar 6.5 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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