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Cited by 67Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromatin Remodeling and Cancer

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

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Yen, Angela, Kellis, Manolis·2015·Nature Communications
DOI 10.1038/ncomms8973PMC PMC4557131
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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.

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Authors
Yen, A., & Kellis, M.
Affiliations
Broad Institute (US)
Corresponding author
Kellis, Manolis
ORCID
Kellis, Manolis
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2015-08-18
Volume
6
Issue
1
Pages
7973-7973
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms8973
PMC
PMC4557131
OpenAlex
W1161512630
Cited by
67
References
73
Citations by year
2026: 3 · 2025: 2 · 2024: 3 · 2023: 7 · 2022: 4 · 2021: 15 · 2020: 9 · 2019: 6 · 2018: 4 · 2017: 8 · 2016: 6
FWCI
2.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
Funders
  • National Science Foundation
  • University of Washington
  • University of British Columbia
  • National Institutes of Health (NIH-R01, 5u54hg004570-04, NIH U54, HG007000)
  • National Human Genome Research Institute (U41HG007000, U54HG006991, RC1HG005334, R01HG004037, HG004570, HG006911)
  • National Institute of General Medical Sciences (R01GM113708)
  • National Institute of Environmental Health Sciences (U01ES017156)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
epigenome, sex differences, tissue type, developmental age, Roadmap Epigenomics, ENCODE, pathway enrichment
MeSH terms
Aging, Cell Differentiation, Chromatin, Female, Gene Expression Regulation, Humans, Male, Sex Factors, Computational Biology, Genetic Predisposition to Disease, Epigenomics

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