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Int J Biol Sci 2011; 7(7):1045-1055. doi:10.7150/ijbs.7.1045

Research Paper

Repertoire of Porcine MicroRNAs in Adult Ovary and Testis by Deep Sequencing

Mingzhou Li1*, Yingkai Liu1*, Tao Wang1, Jiuqiang Guan1, Zonggang Luo1, Haosi Chen2, Xin Wang2, Lei Chen3, Jideng Ma1, Zhiping Mu1, An-an Jiang1, Li Zhu1, Qiulei Lang4, Xiaochuan Zhou4, Jinyong Wang3, Wenxian Zeng5, Ning Li6, Kui Li7, Xiaolian Gao2✉, Xuewei Li1✉

1. Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an, Sichuan, China;
2. Department of Biology & Biochemistry, University of Houston, Houston, Texas, USA;
3. Chongqing Academy of Animal Science, Chongqing, China;
4. LC Sciences, Houston, Texas, USA;
5. College of Animal Science & Technology, Northwest A & F University, Yangling, Shaanxi, China;
6. State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China;
7. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
*These authors contributed equally to this work.

Abstract

Background: MicroRNAs (miRNAs), a large family of short endogenous RNAs known to post-transcriptionally repress gene expression, participate in the regulation of almost every cellular process. Changes in miRNA expression are associated with many pathologies. Ovarian folliculogenesis and testicular spermatogenesis are complex and coordinated biological processes, in which tightly regulated expression and interaction of a multitude of genes could be regulated by these miRNAs. Identification and preliminary characterization of gonad-specific miRNAs would be a prerequisite for a thorough understanding of the role that miRNA-mediated posttranscriptional gene regulation plays in mammalian reproduction.

Method: Here, we present the identification of a repertoire of porcine miRNAs in adult ovary and testis using deep sequencing technology. A bioinformatics pipeline was developed to distinguish authentic mature miRNA sequences from other classes of small RNAs represented in the sequencing data.

Results: Using this approach, we detected 582 precursor hairpins (pre-miRNAs) encoding for 732 mature miRNAs, of which 673 are unique. Statistically, 224 unique miRNAs (out of 673, 33.28%) were identified which had significant differential expression (DE) between ovary and testis libraries (P < 0.001). Most of DE miRNAs located on the X chromosome (X-linked miRNAs) (24 out of 34, 70.59%) significantly up-regulated in ovary versus testis (P < 0.001). Predictably, X-linked miRNAs are expressed in a testis-preferential or testis-specific pattern. To explore the potential for co-expression among genomic location clusters of X-linked miRNAs, we surveyed the relationship between the distance separating miRNA loci and the coordinate expression patterns of 32 high confidence X-linked miRNAs in seven normal pig tissues using the real-time quantitative PCR (q-PCR) approach. Our results show that proximal pairs of miRNAs are generally co-expressed implying that miRNAs within 50 kb of genomic bases are typically derived from a common transcript.

Conclusions: The present study characterizes the miRNA transcriptome of adult porcine gonads, with an emphasis on the co-expression patterns of X-linked miRNAs. Our report should facilitate studies of the organ-specific reproductive roles of miRNAs.

Keywords: pig, miRNA, ovary, testis, deep sequencing

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See http://ivyspring.com/terms for full terms and conditions.
How to cite this article:
Li M, Liu Y, Wang T, Guan J, Luo Z, Chen H, Wang X, Chen L, Ma J, Mu Z, Jiang Aa, Zhu L, Lang Q, Zhou X, Wang J, Zeng W, Li N, Li K, Gao X, Li X. Repertoire of Porcine MicroRNAs in Adult Ovary and Testis by Deep Sequencing. Int J Biol Sci 2011; 7(7):1045-1055. doi:10.7150/ijbs.7.1045. Available from http://www.ijbs.com/v07p1045.htm