Characterization and analysis of differentially expressed microRNAs in hircine ovaries during the follicular and luteal phases

Retinoic acid enhances ovarian steroidogenesis by regulating granulosa cell proliferation and MESP2/STAR/CYP11A1 pathway

INTRODUCTION

Ovarian steroidogenesis not only affects the embryonic development and pregnancy outcome, but also associates with many diseases in mammals and women. Exploring the nutrients and mechanisms influencing ovarian steroidogenesis is critical to maintaining the optimal reproductive performance, as well as guaranteeing body health.

OBJECTIVES

This research aimed to explore the effect of retinol metabolism on ovarian steroidogenesis and the underlying mechanisms.

METHODS

Comparative transcriptomic analysis of ovaries from normal and low reproductive performance sows were performed to identify the main causes leading to low fertility. The metabolites regulating steroid hormones synthesis were investigated in ovarian granulosa cells. Gene interference, overexpression, dual-luciferase reporter assays, chromatin immunoprecipitation and transcriptome analysis were further conducted to explore the underlying mechanisms of Aldh1a1 mediating ovarian steroidogenesis.

RESULTS

Transcriptome analysis of ovaries from normal and low reproductive performance sows showed the significant differences in both retinol metabolism and steroid hormones synthesis, indicating retinol metabolism probably influenced steroid hormones synthesis. The related metabolite retinoic acid was furtherly proven a highly active and potent substance strengthening estrogen and progesterone synthesis in ovarian granulosa cells. For the first time, we revealed that retinoic acid synthesis in porcine and human ovarian granulosa cells was dominated by Aldh1a1, and required the assistance of Aldh1a2. Importantly, we demonstrated that Aldh1a1 enhanced the proliferation of ovarian granulosa cells by activating PI3K-Akt-hedgehog signaling pathways. In addition, Aldh1a1 regulated the expression of transcription factor MESP2, which targeted the transcription of Star and Cyp11a1 through binding to corresponding promoter regions.

CONCLUSION

Our data identified Aldh1a1 modulates ovarian steroidogenesis through enhancing granulosa cell proliferation and MESP2/STAR/CYP11A1 pathway. These findings provide valuable clues for improving ovarian health in mammals.

Human umbilical cord mesenchymal stem cell-derived extracellular vesicles improve ovarian function in rats with primary ovarian insufficiency by carrying miR-145-5p

OBJECTIVE

Stem cell/exosome therapy is a novel strategy for primary ovarian insufficiency (POI). This paper is to examine the role of human umbilical cord mesenchymal stem cell-derived extracellular vesicles (hUCMSC-EVs) in POI.

METHODS

hUCMSC-EVs were extracted and identified. POI rats were induced by cyclophosphamide for 15 days and treated with EV or GW4869 every 5 days and euthanized 28 days later. Vaginal smears were observed for 21 days. Serum hormone levels (FSH/E2/AMH) were measured by ELISA. Ovarian morphology, follicle numbers, and granulosa cell (GC) apoptosis were observed by HE and TUNEL staining. GCs extracted from Swiss albino rats were cyclophosphamide-induced to establish the POI cell model, followed by oxidative injury and apoptosis evaluation with the help of DCF-DA fluorescence, ELISA, and flow cytometry. The relation between miR-145-5p and XBP1 was predicted on StarBase and validated by dual-luciferase assay. miR-145-5p and XBP1 levels were measured by RT-qPCR and Western blot.

RESULTS

EV treatment reduced irregular estrus cycle incidence since day 7, increased E2 and AMH levels and all-stage follicle numbers, reduced FSH level, GC apoptosis, and atretic follicle numbers in POI rats. EV treatment diminished GC oxidative injury and apoptosis in vitro. miR-145-5p knockdown in hUCMSC-EVs partly abolished hUCMSC-EV-mediated effects on GCs and ovarian function in vivo and on GC oxidative injury and apoptosis in vitro. Silencing XBP1 partially negated miR-145-5p knockdown-exerted effects on GCs in vitro.

CONCLUSION

miR-145-5p carried by hUCMSC-EVs attenuates GC oxidative injury and apoptosis and thus extenuates ovarian injury and improves ovarian function in POI rats.

Urinary Cell-Free miR-99a-5p as a Potential Biomarker for Estrus Detection in Buffalo

Accurate estrus detection method is the need of the hour to improve reproductive efficiency of buffaloes in dairy industry, as the currently available estrus detection methods/tools lack high sensitivity and specificity. Recently, circulating miRNAs have been shown as non-invasive biomarkers by various studies. Hence, in order to evaluate their potential as estrus biomarkers, the objective of this study was to identify and compare the levels of 10 hormone-responsive miRNAs in the urine collected at proestrus (PE), estrus (E), and diestrus (DE) phases of buffaloes (n = 3) pertaining to a discovery sample. Among 10 urinary miRNAs, the levels of bta-mir-99a-5p (E/PE 0.5-fold, P < 0.05; DE/PE 1.9-fold), bta-miR-125b (E/PE 0.5-fold; DE/PE 0.7-fold), bta-mir-145 (E/PE 1.5-fold; DE/PE 0.7-fold), bta-mir-210 (E/PE 1.2-fold, DE/PE 0.7-fold), mir-21 (E/PE 1.5-fold, DE/PE 2-fold), and bta-mir-191 (E/PE 1.3-fold; DE/PE 0.8-fold) were found to be altered during different phases of buffalo estrous cycle. In contrast, bta-mir-126-3p, bta-let-7f, bta-mir-16b, and bta-mir-378 were undetected in buffalo urine. Furthermore, a validation study in an independent group of 25 buffalo heifers showed the increased levels of urinary bta-mir-99a-5p during the DE (3.92-fold; P < 0.0001) phase as compared to the E phase. Receiver operating characteristic curve analyses also revealed the ability of urinary miR-99a-5p in distinguishing the E from the DE phase (area under the curve of 0.6464; P < 0.08). In silico analysis further showed an enrichment of miR-99a-5p putative targets in various ovarian signaling pathways, including androgen/estrogen/progesterone biosynthesis and apoptosis signaling, implicating the role of miR-99a-5p in ovarian physiology. In conclusion, significantly lower levels of bta-mir-99a-5p at the E phase than the DE phase in buffalo urine indicate its biomarker potential, which needs to be further explored in a large cohort in the future studies.

Differential molecular and hormonal changes in oocytes, granulosa cells and follicular fluid of pregnant and non-pregnant camels

This study aimed to compare the expression of genes regulating follicles development, survival and steroid hormones secretion in oocytes and granulosa cells (GCs) and study the correlation between their expression and follicular fluid (FF) levels of progesterone (P4) in pregnant and non-pregnant camels. In total, 138 ovarian pairs from slaughtered camels were used. Gene expression and hormonal assay were determined using real-time polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The obtained results revealed that the number of follicles (3-8 mm) was significantly (P < 0.05) lower in pregnant, compared with non-pregnant, camels. P4 level in the FF was significantly (P < 0.05) higher in pregnant, compared with non-pregnant, camels. However, no significant (P > 0.05) difference was noticed in the oestradiol (E2) level. STAR, PTEN, IGF1 and BCL2 mRNA levels were significantly higher in GCs and significantly lower in oocytes of pregnant, compared with non-pregnant, camels. However, follicle-stimulating hormone receptor (FSHR) mRNA level was significantly lower in GCs and oocytes, and the BMP15 mRNA level was significantly lower in oocytes of pregnant, compared with non-pregnant, camels. P4 level in FF was positively correlated with STAR, PTEN, IGF1 and BCL2 mRNA levels in GCs and negatively correlated with BMP15 mRNA levels in oocytes and FSHR mRNA levels in GCs and oocytes of pregnant camels. It could be concluded that pregnancy-induced variations in oocytes and GC expression of BMP15, IGF1, FSHR, STAR, BCL2, and PTEN genes might be associated with a decrease in the number of follicles and an increase in the FF level of P4.

Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene

Background

Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reproduction. However, little is known about the expression characteristics of pineal miRNAs in different reproductive seasons (anestrus and breeding season). Therefore, the expression profiles and regulatory roles of ovine pineal miRNAs were investigated during different reproductive stages using Solexa sequencing technology and dual luciferase reporter assays.

Results

A total of 427 miRNAs were identified in the sheep pineal gland. Significant differences in miRNA expression were demonstrated between anestrus and the breeding season in terms of the frequency distributions of miRNA lengths, number of expressed miRNAs, and specifically and highly expressed miRNAs in each reproductive stage. KEGG analysis of the differentially expressed (DE) miRNAs between anestrus and the breeding season indicated that they are significantly enriched in pathways related to protein synthesis, secretion and uptake. Furthermore, transcriptome analysis revealed that many target genes of DE miRNAs in the ribosome pathway showed relatively low expression in the breeding season. On the other hand, analyses combining miRNA-gene expression data with target relationship validation in vitro implied that miR-89 may participate in the negative regulation of aralkylamine N-acetyltransferase (AANAT) mRNA expression by targeting its 3’UTR at a unique binding site.

Conclusions

Our results provide new insights into the expression characteristics of sheep pineal miRNAs at different reproductive stages and into the negative regulatory effects of pineal miRNAs on AANAT mRNA expression.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07536-y.

miR-130a-3p regulates steroid hormone synthesis in goat ovarian granulosa cells by targeting the PMEPA1 gene

MicroRNAs (miRNAs) are key epigenomic regulators of proliferation, differentiation, and secretion in cells involved in follicular development. We here studied the functional role of one such molecule, miR-130a-3p, in goat ovarian granulosa cells (GCs). High expression of this miRNA was evident in goat GCs by fluorescence in situ hybridization and suppressed estradiol and progesterone secretion from these cells, as determined by ELISA. miR-130a-3p was predicted to have a binding site for the 3' UTR of the prostate transmembrane protein androgen induced 1 gene (PMEPA1), and this was verified by a dual-luciferase reporter assay. PMEPA1 mRNA and protein expression were both found to be regulated by miR-130a-3p in GCs. Moreover, the overexpression or knockdown of PMEPA1 enhanced or suppressed estradiol and progesterone secretion from these cells, respectively. Furthermore, the secretion of estradiol and progesterone did not change significantly after the offsetting of PMEPA1 overexpression in GCs by miR-130a-3p. In summary, our present data indicate that miR-130a-3p inhibits the secretion of estradiol and progesterone in GCs by targeting PMEPA1. Our study thus provides seminal data and important new insights into the regulation of reproductive mechanisms in the nanny goat and other female mammals.

The Roles of the miRNAome and Transcriptome in the Ovine Ovary Reveal Poor Efficiency in Juvenile Superovulation

Simple Summary

Using the technology of juvenile superovulation, more follicles can be acquired in juvenile animals than in adult animals. However, oocytes derived from the follicles of juvenile animals are usually of poor quality, meaning that they have lower levels of subsequent maturation and embryonic development. In the present study, we used an exogenous hormone treatment to stimulate Hu sheep in order to compare the differences in ovarian superovulation effects and serum hormone secretion in juvenile and adult sheep. Differentially expressed microRNA (miRNA) and messenger RNA (mRNA) from the ovaries of juvenile and adult Hu sheep were then investigated using high-throughput sequencing technology to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment. We found that molecules of oar-miR-143 and follicle-stimulating hormone receptor (FSHR), among others, might regulate follicle formation, while oar-miR-485-3p, oar-miR-377-3p, and pentraxin 3 (PTX3), among others, may be associated with oocyte quality. The results will help us to identify miRNAs and mRNAs that could be used to predict ovarian superovulation potential and oocyte quality in the future.

Abstract

Juvenile superovulation can provide a wealth of oocyte material for embryo production, animal cloning, and genetic modification research, but embryos derived from juvenile oocytes show poor efficiency in subsequent developmental capacity. In order to reveal the formation mechanism of large numbers of follicles and poor oocyte quality in juvenile ovaries under superovulation treatment, differentially expressed microRNAs (miRNAs) and messenger RNAs (mRNAs) were characterized and investigated in the ovaries of lambs and adult sheep using high-throughput sequencing technology. The majority of differentially expressed miRNAs (337/358) were upregulated in lamb libraries. The expression levels of mRNAs related to hormone receptors (follicle-stimulating hormone receptor, FSHR; luteinizing hormone/choriogonadotropin receptor, LHCGR; estrogen receptor 1, ESR1), steroid hormone secretion (cytochrome P450 family 11 subfamily A member 1, CYP11A1; cytochrome P450 family 17 subfamily A member 1, CYP17A1; cytochrome P450 family 19 subfamily A member 1, CYP19A1), and oocyte quality (pentraxin 3, PTX3; BCL2 apoptosis regulator, BCL2; caspase 3, CASP3) were significantly different between the lamb and adult libraries. The miRNA aor-miR-143, which targets FSHR, was highly and differentially expressed, and PTX3 was predicted to be targeted by oar-miR-485-3p and oar-miR-377-3p in the ovine ovary. A considerable number of miRNAs were predicted to inhibit ESR1 expression in lamb ovaries. In conclusion, oar-miR-143 and FSHR molecules, among others, might regulate follicle formation, and oar-miR-485-3p, oar-miR-377-3p, and PTX3, among others, may be associated with oocyte quality. These identified miRNAs and mRNAs will be beneficial for the prediction of ovarian superovulation potential and screening of oocytes.

miRNA-26-5p inhibits cyclosporine A-induced overgrowth of gingival fibroblasts by regulating PTEN/PI3K/AKT pathway

We evaluated the effect of cyclosporine A (CsA) administration on the level of miR-26-5p in rat gingival tissues and human gingival fibroblasts (HGFs) by qRT-PCR assay. Further, we conducted Western blotting and immunohistochemical analysis to assess the expressions of PTEN, PI3K, and p-AKT, and evaluated cell proliferation of HGFs by MTT assay. CsA treatment significantly downregulated the expressions of miR-26-5p and PTEN and upregulated the expressions of PI3K and p-AKT in both rat gingival tissues and HGFs. Overexpression of miR-26-5p inhibited CsA-induced overgrowth of HGFs, whereas knockdown of miR-26-5p promoted the overgrowth. PTEN knockdown not only promoted CsA-induced overgrowth of human HGFs but also reversed the repressive effects of miR-26-5p on CsA-induced overgrowth of HGFs. Our results revealed that miRNA-26-5p could repress CsA-induced overgrowth of human HGFs by regulating PTEN/PI3K/AKT pathway.

Integrated analysis of miRNA-mRNA interaction in ovaries of Turpan Black Sheep during follicular and luteal phases

To investigate the regulatory mechanism of the follicular-luteal phase transition in Turpan black sheep (Ovis aries), the genome-wide expression patterns of microRNAs (miRNAs) and genes were investigated in ovaries of six sheep (3 years and single lamb with 3 consecutive births) during follicular and luteal phases of the oestrous cycle. Bioinformatic analysis was used to screen potential miRNAs and genes related to Turpan black sheep ovarian function. RT-qPCR was used to validate the sequencing results. In total, we identified 139 known and 71 novel miRNAs in the two phases with miRNA-seq, and a total of 19 miRNAs were significantly differentially expressed, of which 7 were up-regulated and 12 were down-regulated in the follicular phase compared with luteal phase. A total of 150 genes were significantly differentially expressed, including 63 up-regulated and 87 down-regulated in the follicular phase compared with the luteal phase by RNA-seq data analysis. Those DEGs were significantly enriched in 103 GO terms and several KEGG pathways, including metabolic pathway, ovarian steroidogenesis, steroid hormone biosynthesis and oestrogen signalling pathway. In addition, we created a miRNA-mRNA regulatory network to further elucidate the mechanism of follicular-luteal transition. Finally, we identified key miRNAs and genes including miR-143, miR-99a, miR-150, miR-27a, miR-125b, STAR, STAT1, which might play crucial roles in reproductive hormone biosynthesis and follicular development. The miRNA-mRNA interactive network clearly illustrates molecular basis involving in follicular-luteal transition.

Identification and expression profile of microRNA in seven tissues of the Golden snub-nosed monkey (Rhinopithecus roxellanae)

MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven tissues, with 246 conserved known mature miRNAs and 214 novel mature miRNAs. We determined miRNA abundance and expression in the seven tissues using a Tissue Specificity Index score and found that most novel GSM miRNAs showed a highly tissue-specific expression pattern. In particular, 67 novel miRNAs and the miR-34 family were expressed in abundance only in the lung. Five known miRNAs were highly abundant in digestive organs such as the pancreas and liver, and four novel miRNAs were highly expressed in the heart and muscle. Annotation of target genes of GSM miRNAs indicated that target genes were enriched in many important pathways, such as the HIF-1 signaling pathway and xenobiotic biodegradation-related pathways. Collectively, these results emphasize that miRNAs play important roles in GSM diet and high-elevation adaptation regulation. In summary, this study provides essential information on GSM miRNAs and will benefit further investigations of the function and mechanism of miRNAs in controlling gene expression in the GSM.

Evaluating the effect of TLR4-overexpressing on the transcriptome profile in ovine peripheral blood mononuclear cells

Background

Toll-like receptor 4 (TLR4) plays an important role in the elimination of Gram-negative bacteria infections and the initiation of antiinflammatory response. Using the technology of pronuclear microinjection, genetically modified (GM) sheep with TLR4 overexpression were generated. Previous studies have shown that these GM sheep exhibited a higher inflammatory response to Gram-negative bacteria infection than wild type (WT) sheep. In order to evaluate the gene expression of GM sheep and study the co-expressed and downstream genes for TLR4, peripheral blood mononuclear cells (PBMC) from TLR4-overexpressing (Tg) and wild type (WT) sheep were selected to discover the transcriptomic differences using RNA-Seq.

Result

An average of 18,754 and 19,530 known genes were identified in the Tg and WT libraries, respectively. A total of 338 known genes and 85 novel transcripts were found to be differentially expressed in the two libraries (p < 0.01). A differentially expressed genes (DEGs) enrichment analysis showed that the GO terms of inflammatory response, cell recognition, etc. were significantly (FDR < 0.05) enriched. Furthermore, the above DEGs were significantly (FDR < 0.05) enriched in the sole KEGG pathway of the Phagosome. Real-time PCR showed the OLR1, TLR4 and CD14 genes to be differentially expressed in the two groups, which validated the DEGs data.

Conclusions

The RNA-Seq results revealed that the overexpressed TLR4 in our experiment strengthened the ovine innate immune response by increasing the phagocytosis in PBMC.

Relationships between size, steroidogenesis and miRNA expression of the bovine corpus luteum

In a previous study, a subset of miRNAs were identified the expression of which increases substantially during the follicle-luteal transition in cattle. Here, we investigated the functional involvement of some of these miRNAs (miR-96, miR-182, miR-132, miR-21, miR-378) by determining whether there is an association in vivo between their expression in the corpus luteum (CL), CL size and progesterone production. The two largest and two smallest CL were collected from 12 donor beef heifers on Day 7 following ovarian super-stimulation (Day 0 = 28-32 h after first standing to be mounted). Additionally, the CL and a plasma sample were collected from 29 recipient heifers on Day 15. Luteal expression of miRNAs and mRNAs, and plasma progesterone concentrations were quantified by RT-qPCR and RIA, respectively. There were no differences in the mean expression of any miRNAs examined or the steroidogenic enzymes, STAR or CYP11A1, between the largest and smallest CL in donor heifers (P > 0.1). In addition, there were no significant correlations of luteal volume or weight with any miRNA, CYP11A1 or STAR in donor heifers. However, a correlation (r ≥ 0.5, P ≤ 0.001) existed between the transcript levels of CYP11A1 and STAR in the CL, as well as between each of those and miR-182 levels. In addition, CYP11A1 abundance was moderately correlated (r ≤ 0.4, P < 0.05) with each of miR-96 and miR-378. In recipient heifers, progesterone levels were moderately correlated with luteal weight (r = 0.41, P = 0.03) but not with the expression of any miRNA, CYP11A1 or STAR (P > 0.1). Moreover, luteal CYP11A1 and STAR were correlated (r = 0.6, P ≤ 0.001) with miR-182 as well as with each other, consistent with data in donor heifers. Finally, both CYP11A1 and STAR were moderately correlated (r ≤ 0.5) with miR-132 and, in the case of STAR, with miR-378. In summary, there was no association between either luteal weight/volume or plasma progesterone concentrations and any of the miRNAs analysed in donor and recipient heifers. However, CYP11A1 and STAR transcript levels were significantly correlated with several miRNAs, most notably miR-182, as well as with each other, in luteal tissues from both donor and recipient heifers. This finding confirms results of previous in vitro studies and, importantly, provides the first in vivo evidence of a role of the miR-183-96-182 cluster in regulating luteal steroidogenesis.

Combined microRNAome and transcriptome analysis of follicular phase and luteal phase in porcine ovaries

The aim of this study was to explore the expression difference of miRNAs and mRNAs between the follicular phase (FP) and luteal phase (LP) in porcine ovaries and provide a theoretical basis for the research on mammalian reproductive regulation. RNA-Seq and miRNA-Seq were used to identify differentially expressed genes (DEGs) and miRNAs (DEMs) between the FP and LP in ovaries of six sows (3-year-old Yorkshire pigs with similar weights and same parities). Bioinformatic analysis was used to screen potential genes and miRNAs related to porcine ovarian function. Real-time qualitative PCR was used to validate the sequencing results. RNA-Seq results showed that 3,078 genes were up-regulated, and 1,444 genes were down-regulated in the LP compared with the FP, and DEGs were significantly enriched in 242 Gene Ontology (GO) terms and 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. miRNA-Seq identified 112 DEMs, of which 25 were up-regulated and 87 were down-regulated in the LP compared with the FP. We obtained 186 intersection genes (IGs) between the 4,522 DEGs and 2,444 target genes predicted from the 112 DEMs. After constructing a miRNA-gene-pathway network, we identified key miRNAs and genes including miR-17-3p, miR-214, miR-221-5p, miR-125b, FGF1, YWHAG, YWHAZ, FDFT1 and DHCR24, which are enriched in Hippo and PI3K-Akt signalling pathways, and various metabolic pathways. These results indicate that these key genes and miRNAs may play important roles in the developmental transition from FP to LP in porcine ovaries and represent candidate targets for further study.

Comparative analysis of differentially expressed genes between the ovaries from pregnant and nonpregnant goats using RNA-Seq

Background

A multitude of genes tightly regulate ovarian follicular development and hormone secretion. These complex and coordinated biological processes are altered during pregnancy. In order to further understand the regulatory role of these genes during pregnancy, it is important to screen the differentially expressed genes (DEGs) in the ovaries of pregnant and nonpregnant mammals. To detect the genes associated with the development of pregnancy in goats, DEGs from the ovaries from pregnant and nonpregnant Anhui white goats (pAWGs and nAWGs, respectively) were analyzed using RNA sequencing technology (RNA-Seq).

Results

In this study, 13,676,394 and 13,549,560 clean reads were generated from pAWGs and nAWGs, respectively, and 1724 DEGs were identified between the two libraries. Compared with nAWGs, 1033 genes were upregulated and 691 genes were downregulated in pAWGs, including PGR, PRLR, STAR and CYP19A1, which play important roles in goat reproduction. Gene Ontology analysis showed that the DEGs were enriched for 49 functional GO terms. Kyoto Encyclopedia of Genes and Genomes analysis revealed that 397 DEGs were significantly enriched in 13 pathways, including “cell cycle”, “cytokine–cytokine receptor interaction” and “steroid biosynthesis”, suggesting that the genes may be associated with cell cycle regulation, follicular development and hormone secretion to regulate the reproduction process. Additionally, quantitative real-time PCR was used to verify the reliability of the RNA-Seq data.

Conclusions

The data obtained in this work enrich the genetic resources of goat and provide a further understanding of the complex molecular regulatory mechanisms occurring during the development of pregnancy and reproduction in goats. The DEGs screened in this study may play an important role in follicular development and hormone secretion and they would provide scientific basis for related research in the future.

Electronic supplementary material

The online version of this article (10.1186/s40709-019-0095-9) contains supplementary material, which is available to authorized users.

Discovery and characterization of conserved and novel microRNAs from blunt snout bream (Megalobrama amblycephala) by deep sequencing

MicroRNAs (miRNAs) are short, single stranded RNA molecules with approximately 22 nts in length, which regulate the stability and translation of messenger RNAs in several organisms. To increase the repertoire of miRNAs characterized in M. amblycephala, we used the deep sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the 4 different tissues of M. amblycephala. A total of 309 conserved miRNAs that originated from 131 miRNA families were detected. 15 novel candidates miRNA were identified. Randomly selected 6 miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in 6 different tissues of M. amblycephala. Furthermore, the potential targets were predicted. GO analysis showed that most of the targets were involved in a broad range of physiological functions including fish growth, development, metabolism, stress responses and so on. Overall, our results significantly increased the number of novel miRNAs in M. amblycephala, which should be useful for further investigation into the role of miRNAs in regulating diverse biological processes.