A microRNA expression and regulatory element activity atlas of the mouse immune system

Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD, Aguilar O, Allan R, Arakawa-Hoyt J, Astarita J, Austen KF, Barrett N, Baysoy A, Benoist C, Buechler M, Buenrostro J, Casanova MA, Choi K, Chowdhary K, Colonna M, Crowl T, Deng T, Desai JV, Desland F, Ding J, Dominguez C, Dwyer D, Frascoli M, Gal-Oz S, Goldrath A, Grieshaber-Bouyer R, Jia B, Johanson T, Jordan S, Kang J, Kapoor V, Kenigsberg E, Kim J, Kim Kw, Kiner E, Kronenberg M, Lanier L, Laplace C, Lareau C, Leader A, Lee J, Magen A, Maier B, Maslova A, Mathis D, McFarland A, Meunier E, Monach P, Mostafavi S, Muller S, Muus C, Ner-Gaon H, Nguyen Q, Nigrovic PA, Niizuma K, Novakovsky G, Nutt S, Omilusik K, Ortiz-Lopez A, Paynich M, Peng V, Potempa M, Pradhan R, Quon S, Ramirez R, Ramanan D, Randolph G, Regev A, Seddu K, Shay T, Shemesh A, Shyer J, Smilie C, Spidale N, Subramanian A, Sylvia K, Tellier J, Turley S, Vijaykumar B, Wagers A, Wang C, Wang PL, Yang L, Yim A (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Book Volume: 22

Pages Range: 914-927

Journal Issue: 7

DOI: 10.1038/s41590-021-00944-y

Abstract

To better define the control of immune system regulation, we generated an atlas of microRNA (miRNA) expression from 63 mouse immune cell populations and connected these signatures with assay for transposase-accessible chromatin using sequencing (ATAC–seq), chromatin immunoprecipitation followed by sequencing (ChIP–seq) and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells. miRNA complexity was relatively low, with >90% of the miRNA compartment of each population comprising <75 miRNAs; however, each cell type had a unique miRNA signature. Integration of miRNA expression with chromatin accessibility revealed putative regulatory elements for differentially expressed miRNAs, including miR-21a, miR-146a and miR-223. The integrated maps suggest that many miRNAs utilize multiple promoters to reach high abundance and identified dominant and divergent miRNA regulatory elements between lineages and during development that may be used by clustered miRNAs, such as miR-99a/let-7c/miR-125b, to achieve distinct expression. These studies, with web-accessible data, help delineate the cis-regulatory elements controlling miRNA signatures of the immune system.

Authors with CRIS profile

Involved external institutions

Icahn School of Medicine at Mount Sinai United States (USA) (US) Genentech Inc. United States (USA) (US) University of California, San Diego United States (USA) (US) Massachusetts Institute of Technology (MIT) United States (USA) (US) IMS RIKEN Center for Integrative Medical Sciences Japan (JP) QIAGEN GmbH Germany (DE) Veterans Affairs Healthcare System Boston and Harvard Medical School United States (USA) (US) Brigham and Women's Hospital (BWH) United States (USA) (US) Eli and Edythe L. Broad Institute of MIT and Harvard United States (USA) (US) University of California San Francisco (UCSF) United States (USA) (US) Walter and Eliza Hall Institute of Medical Research (WEHI) Australia (AU) Harvard University United States (USA) (US) Washington University United States (USA) (US) National Institute of Allergy and Infectious Diseases United States (USA) (US) University of Massachusetts Medical School United States (USA) (US) Ben-Gurion University of the Negev (BGU) / אוניברסיטת בן-גוריון בנגב Israel (IL) La Jolla Institute for Immunology United States (USA) (US) University of British Columbia Canada (CA)

How to cite

APA:

Rose, S.A., Wroblewska, A., Dhainaut, M., Yoshida, H., Shaffer, J.M., Bektesevic, A.,... Yim, A. (2021). A microRNA expression and regulatory element activity atlas of the mouse immune system. Nature Immunology, 22(7), 914-927. https://doi.org/10.1038/s41590-021-00944-y

MLA:

Rose, Samuel A., et al. "A microRNA expression and regulatory element activity atlas of the mouse immune system." Nature Immunology 22.7 (2021): 914-927.

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