TY - JOUR
T1 - Common DNA sequence variation influences 3-dimensional conformation of the human genome
AU - Gorkin, David U.
AU - Qiu, Yunjiang
AU - Hu, Ming
AU - Fletez-Brant, Kipper
AU - Liu, Tristin
AU - Schmitt, Anthony D.
AU - Noor, Amina
AU - Chiou, Joshua
AU - Gaulton, Kyle J.
AU - Sebat, Jonathan
AU - Li, Yun
AU - Hansen, Kasper D.
AU - Ren, Bing
N1 - Publisher Copyright:
© 2019 The Author(s).
PY - 2019/11/28
Y1 - 2019/11/28
N2 - 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.
AB - 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.
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U2 - 10.1186/s13059-019-1855-4
DO - 10.1186/s13059-019-1855-4
M3 - Article
C2 - 31779666
AN - SCOPUS:85075727423
VL - 20
JO - Genome Biology
JF - Genome Biology
SN - 1474-7596
IS - 1
M1 - 255
ER -