Global Long Intergenic Non-coding RNA Expression Profiles in Response to Clinical Ketosis in Transition Dairy Cows

Zhou-Lin Wu; Kun Du; Shi-Yi Chen; Xianbo Jia; Jie Wang; Song-Jia Lai

doi:10.29261/pakvetj/2020.101

Zhou-Lin Wu Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China : Key Lab of Meat Processing of Sichuan Province, Chengdu University,Chengdu 610106,China

Kun Du Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China

Shi-Yi Chen Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China

Xianbo Jia Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China

Jie Wang Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China

Song-Jia Lai Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University,Chengdu 611130,China

Many studies showed that long intergenic non-coding RNAs (lincRNAs) have multifaceted roles in various biological processes. However, roles and profiles of lincRNAs in clinical ketosis of dairy cows are still poorly understood. In this study, blood samples of both nine cows affected with clinical ketosis (i.e., case group) and ten healthy ones as control group at 2 weeks before as well as 2 weeks after parturition were collected for genome-wide analysis of lincRNA transcriptome. A total of 2154 novel intergenic transcripts were obtained from all the 38 RNA-Seq libraries, with 795 lincRNAs were identified. By comparing to protein coding transcripts, the characteristics reported in long non-coding RNAs were observed in our identified lincRNAs, such as shorter in transcript length, lower expression level, and fewer exons. Furthermore, we found thirteen differentially expressed lincRNAs (DELs) between case and control group. The cis- and trans-regulatory analysis obtained 124 target genes for these 13 DELs that were functionally involved in metal ion binding, cation binding, biological stress response, and energy metabolism. This study provides a comprehensive expression profile of lincRNAs associated with the progression and onset of clinical ketosis in transition dairy cows, which will facilitate further research on the functional roles of non-coding RNAs on cow ketosis biology.