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Series GSE128678 Query DataSets for GSE128678
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
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.
Overall design Hi-C in 20 lymphoblastoid cell lines with two bilogical replicates
Contributor(s) Gorkin DU, Qiu Y, Hu M, Ren B
Citation(s) 31779666, 32000688
Submission date Mar 21, 2019
Last update date Feb 10, 2020
Contact name Yunjiang Qiu
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (38)
GSM3682164 GM18486 Rep1
GSM3682165 GM18486 Rep2
GSM3682166 GM18505 Rep1
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

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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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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