Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Fangzheng Shang; Yu Wang; Rong Ma; Zhengyang Di; Zhihong Wu; Erhan Hai; Youjun Rong; Jianfeng Pan; Lili Liang; Zhiying Wang; Ruijun Wang; Zhihong Liu; Yanhong Zhao; Zhixin Wang; Jinquan Li; Yanjun Zhang

doi:10.3389/fgene.2021.678825

Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

Front Genet. 2021 Jun 11:12:678825. doi: 10.3389/fgene.2021.678825. eCollection 2021.

Authors

Fangzheng Shang¹, Yu Wang², Rong Ma³, Zhengyang Di¹, Zhihong Wu¹, Erhan Hai¹, Youjun Rong¹, Jianfeng Pan¹, Lili Liang¹, Zhiying Wang¹, Ruijun Wang¹, Zhihong Liu¹, Yanhong Zhao¹, Zhixin Wang¹, Jinquan Li^{2

3

4}, Yanjun Zhang¹

Affiliations

¹ College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
² Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China.
³ Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.
⁴ Engineering Research Center for Goat Genetics and Breeding, Hohhot, China.

Abstract

Background: Inner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells.

Result: In this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA-miRNA-mRNA, and formed a total of 102 pairs of circRNA-miRNA and 126 pairs of miRNA-mRNA interactions. The binding relationship of circRNA3236-chi-miR-27b-3p and circRNA3236-chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship.

Conclusion: To summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA-miRNA-mRNA was constructed and preliminarily verified using DE circRNAs.

Keywords: cashmere goat; circRNA; expression profile; functional analysis; hair follicles.