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| Status |
Public on Oct 02, 2019 |
| Title |
Common DNA sequence variation influences 3-dimensional conformation of the human genome |
| Organism |
Homo sapiens |
| Experiment type |
Other
Third-party reanalysis
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| Summary |
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. To address these questions, we performed Hi-C on Lymphoblastoid Cell Lines (LCLs) from a panel of 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that these conformational variations are often accompanied by variations in gene expression, histone modifications, and transcription factor (TF) 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 (QTLs) 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. 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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| Overall design |
Hi-C in 20 lymphoblastoid cell lines with two bilogical replicates
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| Contributor(s) |
Gorkin DU, Qiu Y, Hu M, Ren B |
| Citation(s) |
31779666, 32000688 |
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| Submission date |
Mar 21, 2019 |
| Last update date |
Feb 10, 2020 |
| Contact name |
Yunjiang Qiu |
| Organization name |
University of California, San Diego
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (38)
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| Relations |
| Reanalysis of |
GSM1181867 |
| Reanalysis of |
GSM1181868 |
| Reanalysis of |
GSM1267196 |
| Reanalysis of |
GSM1267197 |
| Reanalysis of |
GSM1267198 |
| Reanalysis of |
GSM1267199 |
| Reanalysis of |
GSM1267200 |
| Reanalysis of |
GSM1267201 |
| Reanalysis of |
GSM1267202 |
| Reanalysis of |
GSM1267203 |
| Reanalysis of |
GSM1267204 |
| Reanalysis of |
GSM1267205 |
| BioProject |
PRJNA528584 |
| SRA |
SRP189139 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128678_RAW.tar |
6.4 Gb |
(http)(custom) |
TAR (of BW, MAT) |
| GSE128678_bw_file.tar.gz |
104.3 Mb |
(ftp)(http) |
TAR |
| GSE128678_processed_files.tar.gz |
42.5 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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