Integrated Analysis of miRNA and mRNA Expression Profiles Reveals Functional miRNA-Targets in Development Testes of Small Tail Han Sheep

• Published in: G3 : genes - genomes - genetics Vol. 9; no. 2; pp. 523 - 533
• Main Authors: Bai, Man, Sun, Limin, Jia, Chao, Li, Jiarong, Han, Yue, Liu, Hang, Chen, Yang, Jiang, Huaizhi
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01.02.2019; Oxford University Press
• Subjects: Investigations; miRNAs; mRNAs; Small Tail Han Sheep; spermatogenesis; testis development; Small Tail Han Sheep; spermatogenesis; miRNAs; testis development; mRNAs
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.118.200947

Small Tail Han Sheep is a highly valued local breed in China because of their precocity, perennial estrus, and high fecundity. The average annual lambing rate of ewes is as high as 180%-270%, the semen of ram has characteristics of high yield, high density, and good motility. To reveal the key miRNAs and miRNA-targets underlying testis development and spermatogenesis in male Small Tail Han Sheep, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes was performed by RNA-seq technology and bioinformatics methods. The results showed that total of 153 known sheep miRNAs and 2712 novel miRNAs were obtained in 2-，6 - and 12-month-old Small Tail Han Sheep testes; 5, 1, and 4 differentially expressed (DE) known sheep miRNAs, and 132, 105, and 24 DE novel miRNAs were identified in 2- vs 6-, 6- vs 12-, and 2- vs 12-month-old testes, respectively. We combined miRNA results of this study and the mRNA results obtained in our previous study to predict the target mRNAs of DE known sheep miRNAs; 131, 10, and 15 target mRNAs of DE known sheep miRNAs and 76, 1, and 11 DE miRNA-targets were identified in the three groups, respectively. GO and KEGG analyses showed that: in 2- vs 6-month-olds, the target genes of DE known sheep miRNAs were involved in 100 biological processes and 11 signaling pathways; in 6- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 4 biological processes; and in 2- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 17 biological processes and 4 signaling pathways. Three miR-target regulatory networks were constructed based on these DE miRNA-targets. The key miRNA-Targets involved in testis development and spermatogenesis were screened. 6 known sheep miRNAs and 6 novel miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-379-5p with was validated by a dual luciferase reporter gene detection system.