Journal Article

Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

Li, Chen, Liang, Chunnian, Zhang, Xiaolan, Chang, Yongfang, Yan, Ping, Jia, Congjun, Bao, Qi, Wu, Xiaoyun, Bao, Pengjia

2020

Overview

Background Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties. Conclusions This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Animals / Biological activity / Biomedical and Life Sciences / Cashmere / Cattle - genetics / Cattle - metabolism / Comparative analysis / Conservation / Conserved Sequence / Evolution / Follicles / Gene expression / Gene Regulatory Networks / Genes / Genetic aspects / Genomes / Genomics / Growth factors / Hair / Hair Follicle - growth & development / Hair Follicle - metabolism / Hair follicle cycling / Hair follicles / Life Sciences / lncRNA / Microarrays / Microbial Genetics and Genomics / NCBI blast-2.9.0 / Non-coding RNA / Non-human and non-rodent vertebrate genomics / Nucleotide sequence / Observations / Plant Genetics and Genomics / Pluripotency / Properties / Properties (attributes) / Proteomics / Reagents / Research Article / Ribonucleic acid / RNA / RNA, Long Noncoding - genetics / RNA, Long Noncoding - metabolism / Signal transduction / Signaling / Skin / Stem cells / Transcriptome / Vascular endothelial growth factor / Veterinary medicine / Wnt protein / Yak / Yaks