Dataset Information

Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of Oryctolagus cuniculus in Response to Gonadotrophic Stimulation.

ABSTRACT: Molecular mechanisms responsible for gonadotrophic control of ovarian follicle development and ovulation have not been fully delineated. In this study, prepubertal female rabbits were subjected to a combined PMSG/hCG treatment for the induction of follicle maturation and ovulation. Ovaries of 6 does at different time points during gonadotrophic stimulation were collected for histomorphological examination and genome-wide analysis of miRNA and mRNA transcriptomes, and the plasma were separated for detecting melatonin (MT), prostaglandin E2 (PGE2), estradiol (E2), and progesterone (P4) levels. The results suggested that PMSG promoted the development of the reproductive tract by decreasing plasma levels of E2 and slightly increasing those of MT and PGE2 and that hCG induced ovulation and corpus luteum formation by significantly increasing MT, PGE2, and P4 levels. At the transcriptomic level, a total of 1,122 differentially expressed genes (DEGs) and 12 DE miRNAs were identified using three-group comparisons. Meanwhile, pairwise comparisons revealed that 279 and 103 genes as well as 36 and 20 miRNAs were up- and down-regulated during PMSG-stimulated follicle development while 11 and 5 genes as well as 33 and 16 miRNAs were up- and down-regulated during hCG-induced luteinization. KEGG enrichment analysis of the DEGs derived from both three-group- and two-group comparisons as well as the predicted target genes of DE miRNAs highlighted the crucial roles of pathways involving tissue remodeling, energy metabolism, and regulation of cellular functions in mediating gonadotrophin-induced follicle maturation. Specifically, 3 genes including the matrix metallopeptidase 13 (MMP13), protein phosphatase 1 regulatory subunit 3C (PPP1R3C), and solute carrier family 2 member 12 (SLC2A12), together with 2 miRNAs including the miR-205-1 and miR-34c, were predicted to be the promising downstream targets of both PMSG and hCG. Significantly, the miRNA-mRNA interaction pairs containing top 10 up- and down-regulated mRNAs/miRNAs upon PMSG/hCG stimulation were established, and so were those involved in the PI3K-Akt, ECM-receptor interaction, and focal adhesion pathways during PMSG-induced follicle maturation. Finally, qRT-PCR analysis confirmed the results from RNA-Seq and Small RNA-Seq. Our work may contribute to a better understanding of the regulatory mechanisms of gonadotrophins on ovarian follicle development and ovulation.

SUBMITTER: Hu S

PROVIDER: S-EPMC6828822 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of <i>Oryctolagus cuniculus</i> in Response to Gonadotrophic Stimulation.

Hu Shenqiang S Liang Xiaohu X Ren Xufang X Shi Yu Y Su Hang H Li Yanhong Y Du Kun K Wang Jie J Jia Xianbo X Chen Shiyi S Lai Songjia S

Frontiers in endocrinology 20191029

Molecular mechanisms responsible for gonadotrophic control of ovarian follicle development and ovulation have not been fully delineated. In this study, prepubertal female rabbits were subjected to a combined PMSG/hCG treatment for the induction of follicle maturation and ovulation. Ovaries of 6 does at different time points during gonadotrophic stimulation were collected for histomorphological examination and genome-wide analysis of miRNA and mRNA transcriptomes, and the plasma were separated fo ...[more]

PMID: 31736880

Similar Datasets

Project description:Several studies have investigated miRNA and mRNA co-expression to identify regulatory networks at the transcriptional level. A typical finding of these studies is the presence of both negative and positive miRNA-mRNA correlations. Negative correlations are consistent with the expected, faster degradation of target mRNAs, whereas positive correlations denote the existence of feed-forward regulations mediated by transcription factors. Both mechanisms have been characterized at the molecular level, although comprehensive methods to represent miRNA-mRNA correlations are lacking. At present, genome-wide studies are able to assess the expression of more than 1000 mature miRNAs and more than 35,000 well-characterized human genes. Even if studies are generally restricted to a small subset of genes differentially expressed in specific diseases or experimental conditions, the number of potential correlations remains very high, and needs robust multivariate methods to be conveniently summarized by a small set of data.Nonparametric Kendall correlations were calculated between miRNAs and mRNAs differentially expressed in livers of patients with acute liver failure (ALF) using normal livers as controls. Spurious correlations due to the histopathological composition of samples were removed by partial correlations. Correlations were then transformed into distances and processed by multidimensional scaling (MDS) to map the miRNA and mRNA relationships. These showed: (a) a prominent displacement of miRNA and mRNA clusters in ALF livers, as compared to control livers, indicative of gene expression dysregulation; (b) a clustering of mRNAs consistent with their functional annotations [CYP450, transcription factors, complement, proliferation, HLA class II, monocytes/macrophages, T cells, T-NK cells and B cells], as well as a clustering of miRNAs with the same seed sequence; and (c) a tendency of miRNAs and mRNAs to populate distinct regions of the MDS plot. MDS also allowed to visualize the network of miRNA-mRNA target pairs.Different features of miRNA and mRNA relationships can be represented as thematic maps within the framework of MDS obtained from pairwise correlations. The symmetric distribution of positive and negative correlations between miRNA and mRNA expression suggests that miRNAs are involved in a complex bidirectional molecular network, including, but not limited to, the inhibitory regulation of miRNA targets.

Project description:BackgroundIndependent transcriptome profile analyses of miRNAs or mRNAs under conditions of cadmium (Cd) stress have been widely reported in plants. However, a combined analysis of sRNA sequencing expression data with miRNA target expression data to infer the relative activities of miRNAs that regulate gene expression changes resulting from Cd stress has not been reported in rice. To elucidate the roles played by miRNAs in the regulation of changes in gene expression in response to Cd stress in rice (Oryza sativa L.), we simultaneously characterized changes in the miRNA and mRNA profiles following treatment with Cd.ResultsA total of 163 miRNAs and 2,574 mRNAs were identified to be differentially expressed under Cd stress, and the changes in the gene expression profile in the shoot were distinct from those in the root. At the miRNA level, 141 known miRNAs belonging to 48 families, and 39 known miRNAs in 23 families were identified to be differentially expressed in the root and shoot, respectively. In addition, we identified eight new miRNA candidates from the root and five from the shoot that were differentially expressed in response to Cd treatment. For the mRNAs, we identified 1,044 genes in the root and 448 genes in the shoot that were up-regulated, while 572 and 645 genes were down-regulated in the root and shoot, respectively. GO and KEGG enrichment analyses showed that genes encoding secondary, metabolite synthases, signaling molecules, and ABC transporters were significantly enriched in the root, while only ribosomal protein and carotenoid biosynthesis genes were significantly enriched in the shoot. Then 10 known miRNA-mRNA interaction pairs and six new candidate ones, that showed the opposite expression patterns, were identified by aligning our two datasets against online databases and by using the UEA sRNA toolkit respectively.ConclusionsThis study is the first to use high throughput DNA sequencing to simultaneously detect changes in miRNA and mRNA expression patterns in the root and shoot in response to Cd treatment. These integrated high-throughput expression data provide a valuable resource to examine global genome expression changes in response to Cd treatment and how these are regulated by miRNAs.

Dataset Information

Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of Oryctolagus cuniculus in Response to Gonadotrophic Stimulation.

Publications

Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of <i>Oryctolagus cuniculus</i> in Response to Gonadotrophic Stimulation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets