title: Comparison of liver microRNA transcriptomes of Tibetan and Yorkshire pigs by deep sequencing.
abstract: MicroRNAs (miRNAs) play an important role in the modulation of various metabolic processes in the liver, yet little is known about the liver microRNAome (miRNAome) of the Tibetan pig. Here we used the Yorkshire pig as a control to analyze the Tibetan pig-specific liver miRNAome, and for preliminary investigation of differentially expressed miRNAs participating in metabolism. A comprehensive analysis of Tibetan and Yorkshire pig liver miRNAomes by small RNA sequencing identified 362 unique miRNAs. Among these, 304 were co-expressed in both libraries, and 10 and 48 miRNAs were specifically expressed. Differential expression analysis of miRNAs, miRNA target prediction and KEGG analysis revealed that differentially expressed miRNAs were associated mainly with the metabolism of glucose, lipid and protein. Six differentially expressed miRNAs (miR-34a, miR-326, miR-1, miR-335, miR-185 and miR-378) participating in the metabolism of glucose and lipid were identified. Additionally, qPCR results revealed that a lower expression of miR-34a in Tibetan pig liver may promote gluconeogenesis by increasing the expression of Sirtuin type 1 (Sirt1); a lower expression of miR-1 in Tibetan pig liver may promote the synthesis and accumulation of lipid by increasing the expression of Liver X receptor α (LXRα); and a lower expression of miR-185 in Tibetan pig liver may promote the uptake of cholesterol from blood and secretion of bile by increasing the expression of the scavenger receptor class B type I (SR-BI). Our results provide new information and understanding of porcine miRNA profiles, which may help explain the regulatory mechanisms of miRNAs in the metabolic functions of Tibetan pig liver, and provide new biomarkers to assist in the development of Tibetan pig breeding characteristics.
authors.affiliation: Key Laboratory of Bioresource and Eco-Environment, Ministry of Education, Key Laboratory for Animal Disease Prevention and Food Safety of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China.
authors.forename: Yanyue
authors.initials: Y
authors.lastname: Li
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China.
authors.forename: Xiaocheng
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Bioresource and Eco-Environment, Ministry of Education, Key Laboratory for Animal Disease Prevention and Food Safety of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China; School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan 610500, China.
authors.forename: Wen-Kui
authors.initials: WK
authors.lastname: Sun
authors.affiliation: Key Laboratory of Bioresource and Eco-Environment, Ministry of Education, Key Laboratory for Animal Disease Prevention and Food Safety of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China; Department of Biology Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China.
authors.forename: Chi
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Bioresource and Eco-Environment, Ministry of Education, Key Laboratory for Animal Disease Prevention and Food Safety of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China.
authors.forename: Yi-Hui
authors.initials: YH
authors.lastname: Chen
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Zeng
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Chen
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China.
authors.forename: Yiren
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Key Laboratory of Bioresource and Eco-Environment, Ministry of Education, Key Laboratory for Animal Disease Prevention and Food Safety of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan 610064, China. Electronic address: gaorong96@163.com.
authors.forename: Rong
authors.initials: R
authors.lastname: Gao
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China. Electronic address: liuruicau@126.com.
authors.forename: Rui
authors.initials: R
authors.lastname: Liu
authors.affiliation: Sichuan Academy of Animal Science, Chengdu, Sichuan 610066, China. Electronic address: lvxuebin@21cn.com.
authors.forename: Xuebin
authors.initials: X
authors.lastname: Lv
mesh_terms: D000818:Animals; D001483:Base Sequence; D008099:Liver / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D034421:Sus scrofa / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs
keywords: Liver; MiRNAome; MiRNAs; Tibetan pig; Yorkshire pig