ArticleNature communications2020
Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
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- Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction.bioRxiv : the preprint server for biology · 2023Article
- LINE-1 repression in Epstein-Barr virus-associated gastric cancer through viral-host genome interaction.Nucleic acids research · 2023Article
- Prediction of treatment response to antipsychotic drugs for precision medicine approach to schizophrenia: randomized trials and multiomics analysis.Military Medical Research · 2023Article
- Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops.Nature communications · 2022Article
- Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs.Journal of animal science and biotechnology · 2022Article
- Identification of Diagnostic CpG Signatures in Patients with Gestational Diabetes MellitusBioMed research international · 2021Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 4 countries.
Funding
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 ([Formula: see text]), 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.
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Registered trials
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