A comparative profile of the microRNA transcriptome in immature and mature porcine testes using Solexa deep sequencing

Abstract

MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and extensively compare the expression patterns of sexually immature and mature porcine testes. Solexa sequencing of two small RNA libraries derived from immature (30 days) and mature (180 days) pig testis samples yielded over 25 million high-quality reads. Overall, the two developmental stages had significantly different small RNA compositions. A custom data analysis pipeline identified 398 known and ⁄ or homologous conserved porcine miRNAs, 15 novel pig-specific miRNAs and 56 novel candidate miRNAs. We further observed multiple mature miRNA variants and identified a new bidirectional transcribed miRNA locus, ssc-mir-181a. A total of 122 miRNAs were differentially expressed in the immature and mature testes, and 10 were validated using quantitative RT-PCR. Furthermore, GO and KEGG pathway analyses of the predicted miRNA targets further illustrate the likely roles for these differentially expressed miRNAs in spermatogenesis. This study is the first comparative profile of the miRNA transcriptome in immature and mature porcine testes using a deep sequencing approach, and it provides a useful resource for future studies on the role of miRNAs in spermatogenesis and male infertility treatment.

A multi-faceted approach to understanding male infertility: gene mutations, molecular defects and assisted reproductive techniques (ART)

“…In a recent study, high levels of expression of specific miRNAs was observed in low fertility bulls, which could suggest that miRNAs might be responsible for down regulating gene expression and thereby, regulate proteins that have important roles in fertilization and early embryonic development [187]. Other studies revealed significant differences in the expression of miRNAs between immature and mature individuals, suggesting miRNAs have a role in regulating spermatogenesis [188,189]. Special mention needs to be made of miR-322, miR-323, miR-372 and miR-373 that are presumed to be novel oncogenes that participate in the development of human testicular germ cell tumors [190].…”

MicroRNAs in farm animals

“…Combining deep sequencing and computational analysis, 777 unique miRNAs were identified from six prenatal and four postnatal pigs, including 30 tissue-specific miRNAs . Using similar approaches, 15 novel pig-specific miRNAs and 56 novel candidate miRNAs were identified from pig testis (Lian et al, 2012); 57 miRNAs were identified from pig skeletal muscle (Xie et al, 2010); 293 miRNAs were identified from pig adipose tissue (Li et al, 2011a); 215 miRNAs were identified from the backfat of Large White and Chinese Meishan pigs (Chen et al, 2012a); and 89 miRNAs were identified from pig skeletal muscle and adipose tissue (Cho et al, 2010).…”

A Comprehensive Profile of Mature MicroRNA in the Pig

“…(Table 3) Although most research has hitherto been dedicated to miRNA's roles in meat quality, emerging research has evaluated miRNA in other solid tissues in pigs, including, but not limited to, reproduction. Many miRNAs are enriched in reproductive tissues [4,15,17,44] ( Table 3). Others may play a role in differentiating neurons in brain development [3,13,[70][71][72][73].…”

“…The common research strategy on miRNA may include three aims: (i) characterization of miRNAs (including identification of novel miRNAs), (ii) determination of target genes, and (iii) illumination of function of miRNAs and target genes. These strategies have been widely used to describe the miRNAome in various pig tissues, such as muscle [9][10][11][12], brain [13], fat [14], embryo [3], pituitary [15], intestine [16], ovary [17] and testes [4].…”

“…The pig has been used as a model to study various issues, such as reproduction [4], and the neuronal system [5], and is employed as a source of organs and cells in xenotransplantation [6].…”