Ovarian transcriptomic study reveals the differential regulation of miRNAs and lncRNAs related to fecundity in different sheep

Xiangyang Miao,Qingmiao Luo,Huijing Zhao,Xiaoyu Qin

doi:10.1038/srep35299

Xiangyang Miao, Qingmiao Luo + Show 2 more

Open Access

https://doi.org/10.1038/srep35299

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Abstract

miRNAs and lncRNAs, which represent one of the most highly expressed classes of ncRNAs in development, are attracting increasing interest. A variety of regulators is considered to be implicated in sheep species with different fecundity. However, interactions between miRNAs and lncRNAs and changes in the expression of regulatory lncRNAs in sheep fecundity have not yet been reported. To characterize the important roles of miRNAs and lncRNAs and elucidate their regulating networks in sheep prolificacy, a genome-wide analysis of miRNAs and lncRNAs from Small Tail Han sheep of genotypes FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) and from Dorset sheep (Dorset) was performed. An integrated analysis of miRNAs and lncRNAs was performed to study the regulatory function of miRNAs and lncRNAs in fecundity, revealing significantly correlated patterns of expression. Dramatic changes of miRNAs and lncRNAs suggest their critical roles in sheep fecundity. In conclusion, this is the first study performing thorough investigations of regulatory relationships among lncRNAs, miRNA and mRNAs, which will provide a novel view of the regulatory mechanisms involved in sheep fecundity. These results may provide further insight into sheep fecundity and help us to improve sheep prolificacy.

Highlights

Number of all reads Number of bases Number of mapped reads % mapped reads Number of uniquely mapped reads % uniquely mapped reads
Differentially expressed mRNAs, long non-coding RNAs (lncRNAs) and miRNAs were discriminated between two comparison groups (Table 2)
To predict novel miRNA candidates regulating mRNA, RNAfold was applied to predict the secondary structure of the inverted repeat[20]

Summary

Introduction

Number of all reads Number of bases (in Gb) Number of mapped reads % mapped reads Number of uniquely mapped reads % uniquely mapped reads. To investigate the potential role of lncRNAs in regulating sheep fecundity and to build miRNA, mRNA and lncRNA interaction networks in sheep, we performed RNA-seq to identify genome-wide differentially expressed genes (DEGs), miRNAs and lncRNAs in each comparison. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs and target transcripts of miRNAs were conducted. We further constructed miRNA-lncRNA-mRNA interaction networks associated with sheep prolificacy to determine interactions among miRNAs, lncRNAs and mRNAs

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