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Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data
- Source :
- Wu, Y, Qi, T, Wang, H, Zhang, F, Zheng, Z, Phillips-Cremins, J, Deary, I, McRae, A, Wray, N, Zeng, J & Yang, J 2020, ' Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data ', Nature Communications, vol. 11, 2061 . https://doi.org/10.1038/s41467-020-15587-0, Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020), Nature Communications
- Publication Year :
- 2020
-
Abstract
- Promoter-anchored chromatin interactions (PAIs) play a pivotal role in transcriptional regulation. Current high-throughput technologies for detecting PAIs, such as promoter capture Hi-C, are not scalable to large cohorts. Here, we present an analytical approach that uses summary-level data from cohort-based DNA methylation (DNAm) quantitative trait locus (mQTL) studies to predict PAIs. Using mQTL data from human peripheral blood (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n = 1980$$\end{document}n=1980), we predict 34,797 PAIs which show strong overlap with the chromatin contacts identified by previous experimental assays. The promoter-interacting DNAm sites are enriched in enhancers or near expression QTLs. Genes whose promoters are involved in PAIs are more actively expressed, and gene pairs with promoter-promoter interactions are enriched for co-expression. Integration of the predicted PAIs with GWAS data highlight interactions among 601 DNAm sites associated with 15 complex traits. This study demonstrates the use of mQTL data to predict PAIs and provides insights into the role of PAIs in complex trait variation.<br />Promoter-anchored chromatin interaction (PAI) is a mechanism by which gene expression is regulated, but methods to measure PAIs are costly and currently not scalable. Here, the authors develop an approach by which PAIs can be predicted using summary-level data from methylation QTL studies.
- Subjects :
- DNA Replication
Data Analysis
Epigenomics
0301 basic medicine
Quantitative trait loci
Science
General Physics and Astronomy
Computational biology
Quantitative trait locus
Biology
Polymorphism, Single Nucleotide
Chromatin structure
Article
General Biochemistry, Genetics and Molecular Biology
03 medical and health sciences
0302 clinical medicine
Crohn Disease
Humans
Promoter Regions, Genetic
lcsh:Science
Enhancer
Gene
030304 developmental biology
chromatin structure
0303 health sciences
Multidisciplinary
DNA methylation
food and beverages
dNaM
Promoter
General Chemistry
Chromatin
030104 developmental biology
Gene Expression Regulation
epigenomics
quantitative trait loci
lcsh:Q
030217 neurology & neurosurgery
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Wu, Y, Qi, T, Wang, H, Zhang, F, Zheng, Z, Phillips-Cremins, J, Deary, I, McRae, A, Wray, N, Zeng, J & Yang, J 2020, ' Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data ', Nature Communications, vol. 11, 2061 . https://doi.org/10.1038/s41467-020-15587-0, Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020), Nature Communications
- Accession number :
- edsair.doi.dedup.....e2fcecea3ac323c50da5b656bedb8209