title: Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing.
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.
  
  
  METHODS
  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.
authors.affiliation: Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an, Sichuan, China.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
authors.forename: Yingkai
authors.initials: Y
authors.lastname: Liu
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.forename: Jiuqiang
authors.initials: J
authors.lastname: Guan
authors.forename: Zonggang
authors.initials: Z
authors.lastname: Luo
authors.forename: Haosi
authors.initials: H
authors.lastname: Chen
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Jideng
authors.initials: J
authors.lastname: Ma
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Mu
authors.forename: An-an
authors.initials: AA
authors.lastname: Jiang
authors.forename: Li
authors.initials: L
authors.lastname: Zhu
authors.forename: Qiulei
authors.initials: Q
authors.lastname: Lang
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Zhou
authors.forename: Jinyong
authors.initials: J
authors.lastname: Wang
authors.forename: Wenxian
authors.initials: W
authors.lastname: Zeng
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Kui
authors.initials: K
authors.lastname: Li
authors.forename: Xiaolian
authors.initials: X
authors.lastname: Gao
authors.forename: Xuewei
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D010053:Ovary / Q000378:metabolism*; D013091:Spermatogenesis / Q000235:genetics / Q000502:physiology; D034421:Sus scrofa; D013737:Testis / Q000378:metabolism*
chemical_list: D035683:MicroRNAs