Analysis of 13 Cell Types Reveals Evidence for the Expression of Numerous Novel Primate- and Tissue-Specific MicroRNAs


Eric Londin, Thomas Jefferson University
Phillipe Loher, Thomas Jefferson University
Aristeidis G. Telonis, Thomas Jefferson University
Kevin Quann, Thomas Jefferson University
Peter Clark, Thomas Jefferson University
Yi Jing, Thomas Jefferson University
Eleftheria Hatzimichael, Thomas Jefferson University
Yohei Kirino, Thomas Jefferson University
Shozo Honda, Thomas Jefferson University
Michelle Lally, Brown University
Bharat Ramratnam, Brown University
Clay E. S. Comstock, American Association of Cancer Research
Karen E. Knudsen, Thomas Jefferson University
Leonard Gomella, Thomas Jefferson University
George L. Spaeth, Wills Eye Institute
Lisa Hark, Wills Eye Institute
L. Jay Katz, Wills Eye Institute
Agnieszka Witkiewicz, University of Texas Southwestern Medical Center - Dallas
Abdolmohamad Rostami, Thomas Jefferson University
Sergio A. Jimenez, Thomas Jefferson University
Michael A. Hollingsworth, University of Nebraska Medical Center
Jen Jen Yeh, University of North Carolina - Chapel Hill
Chad A. Shaw, Baylor College of Medicine
Steven E. McKenzie, Thomas Jefferson University
Paul Bray, Thomas Jefferson University
Peter T. Nelson, University of KentuckyFollow
Simona Zupo, Azienda Ospedaliera Universitaria San Martino IST, Italy
Katrien Van Roosbroeck, University of Texas M.D. Anderson Cancer Center
Michael J. Keating, University of Texas M.D. Anderson Cancer Center
George A. Calin, University of Texas M.D. Anderson Cancer Center
Charles Yeo, Thomas Jefferson University
Masaya Jimbo, Thomas Jefferson University
Joseph Cozzitorto, Thomas Jefferson University
Jonathan R. Brody, Thomas Jefferson University
Kathleen Delgrosso, Thomas Jefferson University
John S. Mattick, Garvan Institute of Medical Research, Australia
Paolo Fortina, Thomas Jefferson University
Isidore Rigoutsos, Thomas Jefferson University


Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 statistically significant novel mature miRNAs at a false discovery rate of ≤ 0.05 arising from 3,494 novel precursors; 91.5% of these novel miRNAs were identified independently in 10 or more of the processed samples. Analysis of these novel miRNAs revealed tissue-specific dependencies and a commensurate low Jaccard similarity index in intertissue comparisons. Of these novel miRNAs, 1,657 (45%) were identified in 43 datasets that were generated by cross-linking followed by Argonaute immunoprecipitation and sequencing (Ago CLIP-seq) and represented 3 of the 13 tissues, indicating that these miRNAs are active in the RNA interference pathway. Moreover, experimental investigation through stem-loop PCR of a random collection of newly discovered miRNAs in 12 cell lines representing 5 tissues confirmed their presence and tissue dependence. Among the newly identified miRNAs are many novel miRNA clusters, new members of known miRNA clusters, previously unreported products from uncharacterized arms of miRNA precursors, and previously unrecognized paralogues of functionally important miRNA families (e.g., miR-15/107). Examination of the sequence conservation across vertebrate and invertebrate organisms showed 56.7% of the newly discovered miRNAs to be human-specific whereas the majority (94.4%) are primate lineage-specific. Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage- and/or tissue-specific miRNAs that are uncharacterized.

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Notes/Citation Information

Published in Proceedings of the National Academy of Sciences of the United States of America, v. 112, no. 10, p. E1106-E1115.

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Funding Information

This research was supported by the William M. Keck Foundation (I.R.), the Hirshberg Foundation for Pancreatic Cancer Research (I.R.), the Tolz Foundation Weizmann Institute of Science-Thomas Jefferson University Collaboration Program (I.R. and J.R.B.), a Pilot Project Award by the NIH Autoimmune Centers of Excellence (2U19-AI056363-06/20309840 to I.R., S.A.J., and P.F.), NIH-National Cancer Institute Core Grant P30CA56036 (to K.D. and P.F.), and Thomas Jefferson University Institutional funds. J.J.Y. is supported by NIH Grant CA140424. M.L. and B.R. are supported by Lifespan/Tufts/Brown Center for AIDS Research Grant P30 AI042853. P.T.N. is supported by NIH Grants AG042419, NS085830, and AG028383. S.A.J. is supported by NIH/National Institute of Arthritis and Musculoskeletal and Skin Diseases Grant R01 AR 19616. G.A.C. is supported in part by the CLL Global Research Foundation, a Sister Institution Network Foundation MD Anderson Cancer Center-German Cancer Research Center grant on Chronic Lymphocytic Leukemia, the Laura and John Arnold Foundation, the RGK Foundation, and the Estate of C. G. Johnson, Jr. C.Y. is supported by the Jefferson Pancreas, Biliary and Related Cancer Center. P.B. is supported by Grant HL102482 from the National Heart, Lung, and Blood Institute of the National Institutes of Health. K.E.K. is supported by a Pennsylvania Commonwealth Universal Research Enhancement grant and Grant R01 CA099996. Y.K. is supported by NIH grant GM106047. C.E.S.C. was supported by Department of Defense Grant PC094507.