title: Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.
abstract: 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.
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Eric
authors.initials: E
authors.lastname: Londin
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Phillipe
authors.initials: P
authors.lastname: Loher
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Aristeidis G
authors.initials: AG
authors.lastname: Telonis
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Kevin
authors.initials: K
authors.lastname: Quann
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Peter
authors.initials: P
authors.lastname: Clark
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Yi
authors.initials: Y
authors.lastname: Jing
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107; Department of Hematology, University Hospital of Ioannina, Ioannina, GR-45500, Greece;
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Hatzimichael
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Yohei
authors.initials: Y
authors.lastname: Kirino
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Shozo
authors.initials: S
authors.lastname: Honda
authors.affiliation: Department of Medicine, Rhode Island and Miriam Hospitals, Alpert Medical School of Brown University, Providence, RI 02912;
authors.forename: Michelle
authors.initials: M
authors.lastname: Lally
authors.affiliation: Department of Medicine, Rhode Island and Miriam Hospitals, Alpert Medical School of Brown University, Providence, RI 02912;
authors.forename: Bharat
authors.initials: B
authors.lastname: Ramratnam
authors.affiliation: American Association of Cancer Research, Philadelphia, PA 19106;
authors.forename: Clay E S
authors.identifier: http://orcid.org/0000-0001-5867-1489
authors.initials: CE
authors.lastname: Comstock
authors.affiliation: Department of Urology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Karen E
authors.initials: KE
authors.lastname: Knudsen
authors.affiliation: Department of Urology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Leonard
authors.initials: L
authors.lastname: Gomella
authors.affiliation: Glaucoma Service, Wills Eye Institute, Philadelphia, PA 19107;
authors.forename: George L
authors.initials: GL
authors.lastname: Spaeth
authors.affiliation: Glaucoma Service, Wills Eye Institute, Philadelphia, PA 19107;
authors.forename: Lisa
authors.initials: L
authors.lastname: Hark
authors.affiliation: Glaucoma Service, Wills Eye Institute, Philadelphia, PA 19107;
authors.forename: L Jay
authors.initials: LJ
authors.lastname: Katz
authors.affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75235;
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Witkiewicz
authors.affiliation: Department of Neurology, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Abdolmohamad
authors.initials: A
authors.lastname: Rostami
authors.affiliation: Jefferson Institute of Molecular Medicine and The Scleroderma Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Sergio A
authors.initials: SA
authors.lastname: Jimenez
authors.affiliation: Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198;
authors.forename: Michael A
authors.initials: MA
authors.lastname: Hollingsworth
authors.affiliation: Departments of Surgery and Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514;
authors.forename: Jen Jen
authors.initials: JJ
authors.lastname: Yeh
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
authors.forename: Chad A
authors.initials: CA
authors.lastname: Shaw
authors.affiliation: Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Steven E
authors.initials: SE
authors.lastname: McKenzie
authors.affiliation: Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Paul
authors.initials: P
authors.lastname: Bray
authors.affiliation: Department of Pathology, Division of Neuropathology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506;
authors.forename: Peter T
authors.initials: PT
authors.lastname: Nelson
authors.affiliation: Molecular Diagnostic Laboratory, Pathology Department, Istituto di Ricovero e Cura a Carattere Scientifico, Azienda Ospedaliera Universitaria San Martino IST, Genoa, Italy;
authors.forename: Simona
authors.initials: S
authors.lastname: Zupo
authors.affiliation: Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77030;
authors.forename: Katrien
authors.initials: K
authors.lastname: Van Roosbroeck
authors.affiliation: Leukemia Department, University of Texas MD Anderson Cancer Center, Houston, TX 77030;
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Keating
authors.affiliation: Leukemia Department, University of Texas MD Anderson Cancer Center, Houston, TX 77030;
authors.forename: George A
authors.initials: GA
authors.lastname: Calin
authors.affiliation: Department of Surgery, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia PA 19107;
authors.forename: Charles
authors.initials: C
authors.lastname: Yeo
authors.affiliation: Department of Surgery, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia PA 19107;
authors.forename: Masaya
authors.initials: M
authors.lastname: Jimbo
authors.affiliation: Department of Surgery, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia PA 19107;
authors.forename: Joseph
authors.initials: J
authors.lastname: Cozzitorto
authors.affiliation: Department of Surgery, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia PA 19107;
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Brody
authors.affiliation: Cancer Genomics Laboratory, Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Kathleen
authors.initials: K
authors.lastname: Delgrosso
authors.affiliation: Garvan Institute of Medical Research, Sydney NSW 2010, Australia; and St. Vincent's Clinical School and School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
authors.affiliation: Cancer Genomics Laboratory, Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
authors.forename: Paolo
authors.initials: P
authors.lastname: Fortina
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107; Isidore.Rigoutsos@jefferson.edu.
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
mesh_terms: D000818:Animals; D001483:Base Sequence; D055785:Gene Knockdown Techniques; D016678:Genome; D035683:MicroRNAs / Q000235:genetics*; D011323:Primates / Q000235:genetics*; D043244:Ribonuclease III / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D043244:Ribonuclease III
keywords: RNA sequencing; isomIRs; microRNAs; noncoding RNA; transcriptome