Abstract
Long non-coding RNAs (lncRNAs), >200 nt in length, are transcribed from mammalian genomes. They play important regulatory roles in various biological processes; However, the function and expression profile of lncRNAs involved in the development of hair follicles in the fetus, have been relatively under-explored area. To investigate the specific role of lncRNAs and mRNAs that regulate hair follicle development, we herein performed a comprehensive study on the lncRNA and mRNA expression profiles of sheep at multiple embryonic days (E65, E85, E105, and E135) and six lambs aged one week (D7) and one month (D30) using RNA-seq technology. The number of genes (471 lncRNAs and 12,812 mRNAs) differentially expressed and potential targets of differentially expressed lncRNAs were predicted. Differentially expressed lncRNAs were grouped into 10 clusters based on their expression pattern by K-means clustering. Moreover, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that some differentially expressed mRNAs, such as DKK1, DSG4, FOXE1, Hoxc13, SFRP1, SFRP2, and Wnt10A overlapped with lncRNAs targets, and enriched in important hair follicle developmental pathways, including Wnt, TNF, and MAPK signaling pathways. In addition, 9 differentially expressed lncRNAs and 4 differentially expressed mRNAs were validated using quantitative real-time PCR (qRT-PCR). This study helps enrich the Ovis lncRNA databases and provides a comprehensive lncRNA transcriptome profile of fetal and postnatal skin of sheep. Additionally, it provides a foundation for further experiments on the role of lncRNAs in the regulation of hair growth in sheep.
Highlights
Subo Merino Sheep (SBMS), bred in 2014, are an excellent wool sheep breed in China
In order to identify Long non-coding RNAs (lncRNAs) and mRNAs expressed during the development of hair follicles (HFs) in sheep, we constructed 18 cDNA libraries
Several lncRNAs relevant to skin biology have been reported, such as ANCR and SPRY4-IT144, the detailed functional roles of lncRNAs in hair and wool follicle development are based on limited reports and, largely unknown
Summary
Subo Merino Sheep (SBMS), bred in 2014, are an excellent wool sheep breed in China. This breed is well-known for its good quality wool and high wool yield[1]. Wool is produced through various processes by hair follicles (HFs), which are embedded in the skin of sheep[3]. The HF development directly affects the production and quality of sheep wool. The quality and yield of sheep wool can be improved by studying the genes that regulate the development of HF. Considering the complexity of the HF, studies on fetal skin have been valuable for fully identifying differentially expressed genes (DEGs) that appear to be developmentally regulated. RNA-seq has been widely used to identify DEGs and novel transcript units in skin of domestic animals, including sheep[12], goats[13], and cattle[14]
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