Characterization and differential expression of microRNAs in the ovaries of pregnant and non-pregnant goats (Capra hircus)

Abstract

BackgroundOvarian follicular development and hormone secretion are complex and coordinated biological processes which will usually be altered during pregnancy. Ovarian function is tightly regulated by a multitude of genes, and also by some specific miRNAs. It is necessary to identify the differentially expressed miRNAs in the ovaries of pregnant and non-pregnant mammals, in order to further understand the role of miRNA-mediated post-transcriptional regulation in mammalian reproduction. Here, we performed a comprehensive search for hircine miRNAs using two small RNA sequencing libraries prepared from the ovaries of pregnant and non-pregnant goats.Results617 conserved and 7 putative novel miRNAs were identified in the hircine ovaries. A total of 471 conserved miRNAs (76.34%) were co-expressed in both pregnant and non-pregnant libraries, and 90 pregnancy-specific and 56 non-pregnancy-specific conserved miRNAs were identified. Additionally, 407 unique miRNAs (65.96%) were significantly differentially expressed in the pregnant and non-pregnant libraries, of which 294 were upregulated and 113 were downregulated in the pregnant library compared to the non-pregnant library. Further analysis showed that miR-143 was predicted to bind to the target sequences of Frizzled-6 and -3 receptor genes in the Wnt/beta-catenin signaling pathway, and let-7b may target the Activin receptor I and Smad 2/3 genes in the TGF-beta signaling pathway. The expression level of 5 randomly selected miRNAs were analyzed by quantitative real-time PCR (q-PCR), and the results demonstrated that the expression patterns were consistent with the Solexa sequencing results.ConclusionsThe identification and characterization of differentially expressed miRNAs in the ovaries of pregnant and non-pregnant goats provides important information on the role of miRNA in the regulation of the ovarian development and function. This data will be helpful to facilitate studies on the regulation of miRNAs during mammalian reproduction.

Characterization and expression analysis of microRNAs in Qira black sheep and Hetian sheep ovaries using Solexa sequencing

“…Scatter plot and log2-ratio figures were used to show the expression of miRNAs. The procedures used were as follows: 1) to obtain the ex-pression of transcripts per million, the expression of each miRNA in Qira black sheep and Hetian sheep was normalized; 2) using formulas described by previous studies (Huang et al, 2011;Sun et al, 2013;Yuan et al, 2013;Zhang et al, 2013), the fold-change and P values were calculated from the normalized expression.…”

“…Nevertheless, these data add new information to existing data on sheep miRNAs. Similarly, genome-wide miRNA expression profiles have also been examined in whole ovaries from mice (Ro et al, 2007;Mishima et al, 2008), cattle (Hossain et al, 2009;Tripurani et al, 2010;Huang et al, 2011), pig , goat (Zhang et al, 2013), and fetal sheep (Torley et al, 2011); however comparisons across different follicular stages, different stages of the estrous cycle or different breeds were not performed (Hossain et al, 2012b;McBride et al, 2012). Recent studies have also proposed roles for miRNAs in the regulation of follicular development and apoptosis (Baley and Li, 2012;Donadeu et al, 2012).…”

“…Regardless of species, let-7 family, miR-125b, miR-143, miR-145, and miR-199b, miR-21 and miR-99a have been found to be the most commonly abundant miRNA populations within ovaries (Hossain et al, 2009;Tripurani et al, 2010;Huang et al, 2011;Li et al, 2011;Torley et al, 2011;Zhang et al, 2013). The present study also showed that these miRNAs were expressed at high levels in both libraries, and miR-125b, miR-145, and miR-99a were significantly upregulated in Qira black sheep compared to Hetian sheep.…”

“…As a major regulator of gene expression, several studies have used Solexa sequencing to demonstrate that miRNAs play specific roles in ovarian function and ovulation (Baley and Li, 2012;Hossain et al, 2012b). For example, several studies have been undertaken to identify the distinct miRNAs in the ovaries of pregnant and non-pregnant goats (Zhang et al, 2013), 2-week-old and adult mouse ovaries (Ro et al, 2007), adult bovine ovaries (Hossain et al, 2009), bovine fetal ovaries (Tripurani et al, 2010), and new-born mouse ovaries (Ahn et al, 2010). Zhang et al (2013) identified 624 miRNAs using deep sequencing of goat ovary tissue representing both the pregnant and non-pregnant stages, and 407 conserved miRNAs were differentially expressed.…”

“…For example, several studies have been undertaken to identify the distinct miRNAs in the ovaries of pregnant and non-pregnant goats (Zhang et al, 2013), 2-week-old and adult mouse ovaries (Ro et al, 2007), adult bovine ovaries (Hossain et al, 2009), bovine fetal ovaries (Tripurani et al, 2010), and new-born mouse ovaries (Ahn et al, 2010). Zhang et al (2013) identified 624 miRNAs using deep sequencing of goat ovary tissue representing both the pregnant and non-pregnant stages, and 407 conserved miRNAs were differentially expressed. Additionally, a large body of evidence is available on the involvement of miRNAs in follicular development (Kim et al, 2010;Donadeu et al, 2012;McBride et al, 2012), the function of granulosa cells (Sirotkin et al, 2010;Xu et al, 2011), and embryo development (Suh et al, 2010;Baley and Li, 2012;Hossain et al, 2012a).…”