Cited by 184Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyChromatin Remodeling and Cancer

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Genetic determinants of co-accessible chromatin regions in activated T cells across humans

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Gate, Rachel E., Cheng, Christine S., Aiden, Aviva P., Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M. Grace, Subramaniam, Meena, Shamim, Muhammad, Hougen, Kendrick L., Wortman, Ivo, Huang, Su-Chen, Durand, Neva C., Feng, Ting, De Jager, Philip L., Chang, Howard Y., Aiden, Erez Lieberman, Benoist, Christophe, Beer, Michael A., Ye, Chun J., Regev, Aviv·2018·Nature Genetics

DOI 10.1038/s41588-018-0156-2PMC PMC6097927

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Abstract

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.

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Reviewer #3 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation
(2024) · eLife · doi:10.7554/elife.96852.2.sa1
Reviewer #1 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation
(2024) · eLife · doi:10.7554/elife.96852.2.sa3
Author response: Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation
Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Sun, P., Su, C., Campbell, D., et al. (2024) · eLife · doi:10.7554/elife.96852.2.sa0
Reviewer #2 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation
(2024) · eLife · doi:10.7554/elife.96852.2.sa2
eLife Assessment: Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation
Banovich, N. E. (2024) · eLife · doi:10.7554/elife.96852.2.sa4
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Additional file 4 of Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Aygün, N., Liang, D., Crouse, W. L., Keele, G. R., Love, M. I., & Stein, J. L. (2024) · Figshare · doi:10.6084/m9.figshare.26592971
Additional file 5 of Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Aygün, N., Liang, D., Crouse, W. L., Keele, G. R., Love, M. I., & Stein, J. L. (2024) · Figshare · doi:10.6084/m9.figshare.26592974
Additional file 1 of Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Aygün, N., Liang, D., Crouse, W. L., Keele, G. R., Love, M. I., & Stein, J. L. (2024) · Figshare · doi:10.6084/m9.figshare.26592962
Additional file 3 of Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Aygün, N., Liang, D., Crouse, W. L., Keele, G. R., Love, M. I., & Stein, J. L. (2024) · Figshare · doi:10.6084/m9.figshare.26592968
Additional file 2 of Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Aygün, N., Liang, D., Crouse, W. L., Keele, G. R., Love, M. I., & Stein, J. L. (2024) · Figshare · doi:10.6084/m9.figshare.26592965
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Parameter for convolutional neural networks predicting log-transformed counts of ATAC-seq peaks from Calderon et al. 2019
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Authors: Gate, R. E., Cheng, C. S., Aiden, A. P., Siba, A., Tabaka, M., Lituiev, D., Machol, I., Gordon, M. G., Subramaniam, M., Shamim, M., Hougen, K. L., Wortman, I., Huang, S.-C., Durand, N. C., Feng, T., De Jager, P. L., Chang, H. Y., Aiden, E. L., Benoist, C., Beer, M. A., Ye, C. J., & Regev, A.
Affiliations: University of California, San Francisco (US)
Broad Institute (US)
Baylor College of Medicine (US)
Johns Hopkins University (US)
Harvard University (US)
Stanford University (US)
Corresponding author: Cheng, Christine S.
Ye, Chun J.
Regev, Aviv
ORCID: Cheng, Christine S.
Aiden, Aviva P.
Tabaka, Marcin
Lituiev, Dmytro
Machol, Ido
Gordon, M. Grace
Subramaniam, Meena
Shamim, Muhammad
Durand, Neva C.
Feng, Ting
De Jager, Philip L.
Chang, Howard Y.
Aiden, Erez Lieberman
Benoist, Christophe
Beer, Michael A.
Ye, Chun J.
Regev, Aviv
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2018-07-09
Volume: 50
Issue: 8
Pages: 1140-1150
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/s41588-018-0156-2
PMC: PMC6097927
OpenAlex: W2837542075
Cited by: 181
References: 83
Citations by year: 2026: 10 · 2025: 19 · 2024: 43 · 2023: 22 · 2022: 19 · 2021: 25 · 2020: 23 · 2019: 19 · 2018: 1
FWCI: 6.05
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Institutes of Health (5rm1hg006193-10)
National Human Genome Research Institute (U01HG012192, RM1‐HG006193, P50HG007735, U01HG009380, R01HG007348)
National Cancer Institute (F32CA168253)
National Institute of General Medical Sciences (T32GM067547)
National Institute of Allergy and Infectious Diseases (R21AI133337)
National Institute of Diabetes and Digestive and Kidney Diseases (F32DK096822)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR071522)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords: CD4+ T cells, cis-regulatory elements, chromatin accessibility, 3D genome organization, transcription factor binding sites, gene expression regulation, non-coding variants, T cell activation
MeSH terms: Adult, Autoimmune Diseases, Chromatin, Female, Gene Expression Regulation, Genotype, Humans, Male, Regulatory Sequences, Nucleic Acid, CD4-Positive T-Lymphocytes, Polymorphism, Single Nucleotide

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Genetic determinants of co-accessible chromatin regions in activated T cells across humans

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