Profiling and Functional Analysis of long non-coding RNAs in yak healthy and atretic follicles

Yilong Yao; Zhaoyi Meng; Wangchang Li; Yefen Xu; Yunlu Wang; Sizhu Suolang; Guangyin Xi; Lei Cao; Min Guo

doi:10.1590/1984-3143-AR2021-0131

Profiling and Functional Analysis of long non-coding RNAs in yak healthy and atretic follicles

Anim Reprod. 2022 Oct 24;19(3):e20210131. doi: 10.1590/1984-3143-AR2021-0131. eCollection 2022.

Authors

Yilong Yao^{1

2}, Zhaoyi Meng^{1

3}, Wangchang Li², Yefen Xu^{1

3}, Yunlu Wang^{1

3}, Sizhu Suolang¹, Guangyin Xi⁴, Lei Cao¹, Min Guo⁴

Affiliations

¹ Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.
² Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Beijing, China.
³ Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.
⁴ College of Animal Sciences and Technology, China Agricultural University, Haidian, Beijing, China.

Abstract

Yak is the livestock on which people live in plateau areas, but its fecundity is low. Follicular development plays a decisive role in yak reproductive performance. As an important regulatory factor, the expression of long non-coding RNA (lncRNAs) in yak follicular development and its regulatory mechanism remains unclear. To explore the differentially expressed lncRNAs between healthy and atretic follicular in yaks. We used RNA-seq to construct lncRNA, miRNA, and mRNA expression profiles in yak atretic and healthy follicles, and the RNA sequence results were identified by qPCR. In addition, the correlation of lncRNA and targeted mRNA was also analyzed by Starbase software. Moreover, lncRNA/miRNA/mRNA networks were constructed by Cytoscape software, and the network was verified by dual-luciferase analysis. A total of 682 novel lncRNAs, 259 bta-miRNAs, and 1704 mRNAs were identified as differentially expressed between healthy and atretic follicles. Among them, 135 mRNAs were positively correlated with lncRNA expression and 97 were negatively correlated, which may be involved in the yak follicular development. In addition, pathway enrichment analysis of differentially expressed lncRNA host genes by Kyoto Genome Encyclopedia (KEGG) showed that host genes were mainly involved in hormone secretion, granulosa cell apoptosis, and follicular development. In conclusion, we identified a series of novel lncRNAs, constructed the lncRNA ceRNA regulatory network, and provided comprehensive resources for exploring the role of lncRNAs in yak ovarian follicular development.

Keywords: RNA-seq; atretic follicles; healthy follicles; lncRNA; yak.

Grants and funding

Financial support: The works was supported by the National Natural Science Foundation of China [grant number 3196200115], Ministry of Finance and Ministry of Agriculture and Rural Areas "national modern agricultural industrial technology system (CARS-37)", Key Projects of the Science and Technology Department of Tibet Autonomous Region [grant number: 2019].