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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
Open accessAbstract
Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.
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“Mapping interactions between enhancers and promoters in disease-relevant cells improves the accuracy of the assignment (Grubert et al., 2015; McGeachie et al., 2016; Pomerantz et al., 2009), but this is not always feasible.”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Grubert et al., 2015
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“We have analyzed our ChIA-PET data using two analytical approaches: one that estimates the background contact frequency based on the genomic proximity bias (Mango pipeline) adapted from previous reports (24, 30, 40), and an analytical approach that estimates the background contact frequency based on the ligation frequ…”
BackgroundMethodComprehensive functional genomic resource and integrative model for the human brain
Wang, D., Liu, S., Warrell, J., Won, H., Shi, X., Navarro, F. C. P., Clarke, D., Gu, M., Emani, P., Yang, Y. T., et al. (2018) · Science · doi:10.1126/science.aat8464 · Cited by 965
Metadata
- Authors
- Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., Heidari, N., Euskirchen, G., Huber, W., Pritchard, J. K., Bustamante, C. D., Steinmetz, L. M., Kundaje, A., & Snyder, M.
- Affiliations
- Stanford Medicine (US)
- European Molecular Biology Laboratory (DE)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Snyder, Michael
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-08
- Volume
- 162
- Issue
- 5
- Pages
- 1051-1065
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4556133
- OpenAlex
- W2112673809
- Cited by
- 319
- References
- 56
- Citations by year
- 2026: 12 · 2025: 13 · 2024: 18 · 2023: 21 · 2022: 25 · 2021: 23 · 2020: 37 · 2019: 39 · 2018: 48 · 2017: 39 · 2016: 36 · 2015: 8
- FWCI
- 18.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Heart, Lung, and Blood Institute (R01HL122887, U01HL107393)
- National Human Genome Research Institute (U41HG007000, U54HG006996, R00HG008662, K99HG008662, U41-HG007000-02S1, P50HG007735, U01HG007919, P01HG000205, T32HG000044)
- National Institute of General Medical Sciences (T32GM007790, T32GM007205)
- National Institute of Environmental Health Sciences (R01ES025009)
- U.S. National Library of Medicine (LM 07033, T15LM007033)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- histone modifications, chromatin state, long-range chromatin interactions, topologically associating domains, non-coding variants, gene expression regulation, lymphoblastoid cell lines, Hi-C, ChIA-PET
- MeSH terms
- Cell Line, Chromatin, Chromosomes, Human, Female, Histones, Humans, Lymphocytes, Male, Cohort Studies, Human Genome Project, Quantitative Trait Loci, Regulatory Elements, Transcriptional, Gene Regulatory Networks, Genome-Wide Association Study
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