Cited by 334Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyEpigenetics and DNA Methylation

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Index and biological spectrum of human DNase I hypersensitive sites

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Meuleman, Wouter, Muratov, Alexander, Rynes, Eric, Halow, Jessica, Lee, Kristen, Bates, Daniel, Diegel, Morgan, Dunn, Douglas, Neri, Fidencio, Teodosiadis, Athanasios, Reynolds, Alex, Haugen, Eric, Nelson, Jemma, Johnson, Audra, Frerker, Mark, Buckley, Michael, Sandstrom, Richard, Vierstra, Jeff, Kaul, Rajinder, Stamatoyannopoulos, John·2020·Nature

DOI 10.1038/s41586-020-2559-3PMC PMC7422677

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Abstract

DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA 1–5 and contain genetic variations associated with diseases and phenotypic traits 6–8 . We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA. Here we show that these maps highly resolve the cis -regulatory compartment of the human genome, which encodes unexpectedly diverse cell- and tissue-selective regulatory programs at very high density. These programs can be captured comprehensively by a simple vocabulary that enables the assignment to each DHS of a regulatory barcode that encapsulates its tissue manifestations, and global annotation of protein-coding and non-coding RNA genes in a manner orthogonal to gene expression. Finally, we show that sharply resolved DHSs markedly enhance the genetic association and heritability signals of diseases and traits. Rather than being confined to a small number of distal elements or promoters, we find that genetic signals converge on congruently regulated sets of DHSs that decorate entire gene bodies. Together, our results create a universal, extensible coordinate system and vocabulary for human regulatory DNA marked by DHSs, and provide a new global perspective on the architecture of human gene regulation.

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Authors: Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., Reynolds, A., Haugen, E., Nelson, J., Johnson, A., Frerker, M., Buckley, M., Sandstrom, R., Vierstra, J., Kaul, R., & Stamatoyannopoulos, J.
Affiliations: Altius Institute for Biomedical Sciences (US)
University of Washington (US)
Corresponding author: Meuleman, Wouter
Stamatoyannopoulos, John
ORCID: Meuleman, Wouter
Rynes, Eric
Lee, Kristen
Bates, Daniel
Teodosiadis, Athanasios
Reynolds, Alex
Haugen, Eric
Nelson, Jemma
Frerker, Mark
Buckley, Michael
Sandstrom, Richard
Vierstra, Jeff
Kaul, Rajinder
Stamatoyannopoulos, John
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2020-07-29
Volume: 584
Issue: 7820
Pages: 244-251
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-020-2559-3
PMC: PMC7422677
OpenAlex: W3046013264
Cited by: 331
References: 60
Citations by year: 2026: 40 · 2025: 59 · 2024: 61 · 2023: 58 · 2022: 56 · 2021: 43 · 2020: 14
Type: paratext
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Human Genome Research Institute (U54HG007010, UM1HG009444, R35HG011317)
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 › Epigenetics and DNA Methylation
Keywords: DNase I hypersensitive sites, cis-regulatory elements, genetic association signals, heritability
MeSH terms: Chromatin, Deoxyribonuclease I, DNA, Gene Expression Regulation, Genes, Humans, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Genome, Human, Molecular Sequence Annotation

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