Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.
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Abstract | Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale. |
Year of Publication | 2015
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Journal | Nat Commun
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Volume | 6
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Pages | 7973
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Date Published | 2015 Aug 18
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ISSN | 2041-1723
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URL | |
DOI | 10.1038/ncomms8973
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PubMed ID | 26282110
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PubMed Central ID | PMC4557131
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Grant list | RC1 CA147187 / CA / NCI NIH HHS / United States
R01 GM113708 / GM / NIGMS NIH HHS / United States
R01 HG004037 / HG / NHGRI NIH HHS / United States
U41 HG007000 / HG / NHGRI NIH HHS / United States
U54 HG006991 / HG / NHGRI NIH HHS / United States
HG006911 / HG / NHGRI NIH HHS / United States
HG004570 / HG / NHGRI NIH HHS / United States
RC1-HG005334 / HG / NHGRI NIH HHS / United States
5U01ES017156 / ES / NIEHS NIH HHS / United States
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