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

Abstract

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.

Integrated analysis of miRNAs and mRNA profiling reveals the potential roles of miRNAs in sheep hair follicle development

“…Gene expression is regulated by noncoding RNAs, including miRNAs. MiRNAs, which are endogenously expressed in mammals [32][33][34], are 18-22-nucleotide (nt), small noncoding RNAs that are evolutionarily conserved and negatively regulate the expression of target mRNAs mainly by repressing translation or, in some cases, by cleaving mRNA transcripts [35,36]. miRNAs play a key role in many biological processes by regulating gene expression at the posttranscriptional level.…”

Whole blood transcriptome profiling identifies candidate genes associated with alopecia in male giant pandas (Ailuropoda melanoleuca)

“…The miR-29 family was reported to inhibit the Wnt and BMP signaling pathways causing eventual hair loss and alopecia [ 49 ]. The Wnt was reported to be involved in the hair follicle cycle in yaks ( Bos grunniens ) via mRNA and lncRNA analysis [ 50 , 51 ]. FZD8 (frizzled class receptor 8) as Wnt family receptor, was found to be expressed in dermal papillae cells that controlled feather regeneration in chickens [ 52 ].…”

Identification of the Key Genes Associated with the Yak Hair Follicle Cycle

“…The data in this study used previous preliminary transcriptome sequencing results [ 19 , 20 ]. Additionally, the data also can be obtained from the public dataset PRJNA550233 in the National Center for Biotechnology Information (NCBI) BioProject ( , accessed on 20 October 2020).…”

“…The significantly seasonal change of the HFs in yak is important for its adaptability to alpine environment, which also makes yak an excellent model for the study of HFs cycle. In our previous works, transcriptome data, including mRNA and lncRNA, were measured in yak scapular skin at five time points (Jan., Mar., Jun., Aug., Oct.) during the HFs cycle, and the transcription characteristics and expression were, respectively, analyzed [ 19 , 20 ]. These five time points represent the critical stages during yak hair follicle cycling, among which, Jan. and Mar.…”