Common DNA sequence variation influences 3-dimensional conformation of the human genome
Genome Biol. 2019-11-28;20(1):255.
- Abstract
- Background: The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. Results: To address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. Conclusion: Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized.
- Datasets
- DSR223YLL, DSR170YXE, DSR656RCL, DSR308EDS, DSR417NUY, DSR796CMR, DSR429KPP, DSR202QFC, DSR237SXW, DSR242EAO, DSR658HOF, DSR516LWO, DSR353VNN, DSR064XLC, DSR834JIS, DSR535IPU, DSR152JOK, DSR283EYW, DSR037KWU, DSR264ATN, DSR938WGD, DSR434ECE, DSR592EDG, DSR741WRB, DSR775WNA, DSR666UYW, DSR238UOQ, DSR013CBD, DSR146CIT, DSR072QSU, DSR102WHJ, DSR979FHO, DSR415KYD, DSR853NLS, DSR005FVU, DSR702TLP, DSR495ACZ, DSR672FLT
Related data
- Available data
- website
- Data summary
- All raw sequencing data and many processed data files are available through NCBI’s Gene Expression Omnibus (GEO) accession GSE128678 [78], as well as through the 4D Nucleome data portal.
- Available data
- website
- Data summary
- Additional processed data are available on the Ren lab’s website, or by request.
- Available data
- website
- Data summary
- The following third-party datasets were also used in this study (also listed in Additional file 2: Table S2): GSE48592 [79], GSE52457 [80], GSE63525 [81], GSE50893 [82], GSE47991 [83], GSE62742 [84], E-ERAD-141 [85], and GSE31388 [86]. Code is available at Zenodo accession 3475719 [87], and released under a Common Development and Distribution License compliant with OSI (http://opensource.org/licenses).