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A cell atlas of chromatin accessibility across 25 adult human tissues

Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, View ORCID ProfileJoshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren
doi: https://doi.org/10.1101/2021.02.17.431699
Kai Zhang
1Ludwig Institute for Cancer Research, La Jolla, CA, USA
6Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
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James D. Hocker
1Ludwig Institute for Cancer Research, La Jolla, CA, USA
2Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
3Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
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Michael Miller
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
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Xiaomeng Hou
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
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Joshua Chiou
3Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
5Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
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  • ORCID record for Joshua Chiou
Olivier B. Poirion
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
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Yunjiang Qiu
1Ludwig Institute for Cancer Research, La Jolla, CA, USA
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Yang E. Li
1Ludwig Institute for Cancer Research, La Jolla, CA, USA
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Kyle J. Gaulton
5Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
7Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
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Allen Wang
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
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Sebastian Preissl
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
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Bing Ren
1Ludwig Institute for Cancer Research, La Jolla, CA, USA
4Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
6Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
7Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
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  • For correspondence: biren@health.ucsd.edu
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SUMMARY

Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of human gene regulatory elements in diverse cell types and tissues in the human body, we applied single cell chromatin accessibility assays to 25 distinct human tissue types from multiple donors. The resulting chromatin maps comprising ∼500,000 nuclei revealed the status of open chromatin for over 750,000 candidate cis-regulatory elements (cCREs) in 54 distinct cell types. We further delineated cell type-specific and tissue-context dependent gene regulatory programs, and developmental stage specificity by comparing with a recent human fetal chromatin accessibility atlas. We finally used these chromatin maps to interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues and organ systems.

Competing Interest Statement

Bing Ren is a co-founder, consultant of Arima Genomics and co-founder of Epigenome Technologies, Inc.

Footnotes

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165659

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted February 17, 2021.
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A cell atlas of chromatin accessibility across 25 adult human tissues
Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren
bioRxiv 2021.02.17.431699; doi: https://doi.org/10.1101/2021.02.17.431699
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A cell atlas of chromatin accessibility across 25 adult human tissues
Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren
bioRxiv 2021.02.17.431699; doi: https://doi.org/10.1101/2021.02.17.431699

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