Identification and characterization of circRNAs in the skin during wool follicle development in Aohan fine wool sheep

Ranran Zhao,Lanlan Li,Hegang Li,Jifeng Liu,Fuhui Han,Guoyi Wang,Jianning He,Nan Liu

doi:10.1186/s12864-020-6599-8

Abstract

BackgroundAohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Circular RNAs (circRNAs) are widely expressed non-coding RNAs that can act as competitive endogenous RNAs (ceRNAs) to bind to miRNAs. Although circRNAs have been studied in many fields, research on their activity in sheep wool follicles is limited. To understand the regulation of circRNAs in the growth of fine wool in sheep, we used RNA-Seq to identify circRNAs in sheep shoulder skin samples at three developmental stages: embryonic day 90 (E90d), embryonic day 120 (E120d), and at birth (Birth).ResultsWe identified 8753 circRNAs and found that 918 were differentially-expressed. We then analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified the source genes of circRNAs, which were mainly enriched in cellular component organization, regulation of primary metabolic processes, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and eight miRNAs, using miRanda software. Based on the significant pathways, we speculate that circ_0005720, circ_0001754, circ_0008036, circ_0004032, circ_0005174, circ_0005519, and circ_0007826 might play an important role in regulating wool follicle growth in AFWS. Seven circRNAs were randomly selected to validate the RNA-Seq results, using qRT-PCR.ConclusionOur results provide more information about circRNAs regulation of wool follicle development in AFWS, and establish a solid foundation for future research.

Highlights

Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China
Many studies in recent years have indicated that non-coding RNAs act as important post-transcriptional regulators of gene expression during hair follicle development, including microRNAs, circular RNAs, and long noncoding RNAs
Based on their location in the genome, the 8,753 circRNAs were classified into six types: (1) Classic: when the formation site of the circRNA is exactly on the boundaries of exons (83.4%); (2) Alter-exon: when one end of the circRNA formation site is on the exon boundary, and the other end is inside the exon (8.6%); (3) Intron: when the formation site of the circRNA is completely in the intron region (1.2%); (4) Overlap-exon: when the formation site of the circRNA spans the exon region (5.5%); (5) Antisense: when the circRNA is formed by the antisense strand of the gene (0.3%); (6) Intergenic: when the formation site of circRNA is completely inside the intergenic region (1.0%) (Figure 2b)

Summary

Introduction

Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Wool grows from hair follicles (HF), and its yield and quality are closely related to the development of wool follicles. It is a complex organ of the skin that is capable of self-regeneration, and its structure plays a very important role in its periodic growth process. Many studies in recent years have indicated that non-coding RNAs act as important post-transcriptional regulators of gene expression during hair follicle development, including microRNAs (miRNAs), circular RNAs (circRNAs), and long noncoding RNAs (lncRNAs). Non-coding RNA has been shown to regulate wool fineness and growth of secondary hair follicles in cashmere goats [3]

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