Next Article in Journal
Lentivirus-Mediated ERK2 siRNA Reduces Joint Capsule Fibrosis in a Rat Model of Post-Traumatic Joint Contracture
Previous Article in Journal
Ultrastructural Analysis of Nanogold-Labeled Cell Surface Microvilli in Liquid by Atmospheric Scanning Electron Microscopy and Their Relevance in Cell Adhesion
Int. J. Mol. Sci. 2013, 14(10), 20820-20832; doi:10.3390/ijms141020820
Article

Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data

1,2
, 2
, 2
, 1
, 1
, 1
, 1
 and 2,*
Received: 16 July 2013; in revised form: 22 September 2013 / Accepted: 9 October 2013 / Published: 16 October 2013
(This article belongs to the Section Molecular Pathology)
View Full-Text   |   Download PDF [306 KB, updated 19 June 2014; original version uploaded 19 June 2014]   |   Browse Figures
Abstract: Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system.
Keywords: genome-wide; miRNA; mammalian genome; synteny; deep sequencing genome-wide; miRNA; mammalian genome; synteny; deep sequencing
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Yuan, Z.; Liu, H.; Nie, Y.; Ding, S.; Yan, M.; Tan, S.; Jin, Y.; Sun, X. Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data. Int. J. Mol. Sci. 2013, 14, 20820-20832.

AMA Style

Yuan Z, Liu H, Nie Y, Ding S, Yan M, Tan S, Jin Y, Sun X. Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data. International Journal of Molecular Sciences. 2013; 14(10):20820-20832.

Chicago/Turabian Style

Yuan, Zhidong; Liu, Hongde; Nie, Yumin; Ding, Suping; Yan, Mingli; Tan, Shuhua; Jin, Yuanchang; Sun, Xiao. 2013. "Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data." Int. J. Mol. Sci. 14, no. 10: 20820-20832.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert