Format

Send to

Choose Destination
Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1106-15. doi: 10.1073/pnas.1420955112. Epub 2015 Feb 23.

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

Author information

1
Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
2
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;
3
Department of Medicine, Rhode Island and Miriam Hospitals, Alpert Medical School of Brown University, Providence, RI 02912;
4
American Association of Cancer Research, Philadelphia, PA 19106;
5
Department of Urology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
6
Glaucoma Service, Wills Eye Institute, Philadelphia, PA 19107;
7
Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75235;
8
Department of Neurology, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
9
Jefferson Institute of Molecular Medicine and The Scleroderma Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
10
Department of Biochemistry and Molecular Biology, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198;
11
Departments of Surgery and Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514;
12
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
13
Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107;
14
Department of Pathology, Division of Neuropathology, Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506;
15
Molecular Diagnostic Laboratory, Pathology Department, Istituto di Ricovero e Cura a Carattere Scientifico, Azienda Ospedaliera Universitaria San Martino IST, Genoa, Italy;
16
Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX 77030;
17
Leukemia Department, University of Texas MD Anderson Cancer Center, Houston, TX 77030;
18
Department of Surgery, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia PA 19107;
19
Cancer Genomics Laboratory, Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
20
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.
21
Computational Medicine Center, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA 19107; Isidore.Rigoutsos@jefferson.edu.

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.

KEYWORDS:

RNA sequencing; isomIRs; microRNAs; noncoding RNA; transcriptome

PMID:
25713380
PMCID:
PMC4364231
DOI:
10.1073/pnas.1420955112
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center