The Identification, Expression Characteristics And Functional Regulatory Network Of LncRNAs In The Secondary Hair Follicles Of Liaoning Cashmere Goats

Liaoning cashmere goat is a unique breed of livestock resources used for meat and cashmere in China.The cashmere from secondary hair follicles(SHFs)of cashmere goat can bring great economic benefits to the herders.Long non-coding RNA(lncRNAs)is a class of eukaryotic transcripts with a length of more than 200 bp.They contribute to the regulation of gene expressions involved in multiple processes including the skin cell proliferation,differentiation,and reconstruction of the secondary hair follicles(SHFs).These include Lnc RNA-HOTAIR transcript transcribed from the antisense strand within the HOXC gene cluster.In this investigation,the SHFs of Liaoning cashmere goat were taken as the research object.According to the expression sequence tags(ESTs)in the NCBI database,16 lncRNAs and lnc RNA-HOTAIR transcript were identified,and their molecular expression characteristics and transcriptional patterns were analyzed.The construction of different regulatory networks revealed their complex regulatory relationships with potential target molecules.The specific research content is as follows:In this investigation,first of all,we isolated and identified 16 putative lncRNAs from SHFs of Liaoning cashmere goat based on ESTs in the NCBI database.Also,we analyzed their molecular expression characteristics and transcriptional patterns,and constructed ce RNA regulatory network of newly identified lncRNAs with their potential target molecules during anagen and telogen phases,respectively.The study found that four lncRNAs(lnc RNA-475074,-052149,-052140 and-051789)were significantly up-regulated during anagen,and nine putative lncRNAs(lnc RNA-711032,-475083,-475070,-052139,-052127,-052037,-051903,-051847,-051804)were significantly up-regulated during telogen.The ce RNA regulatory networks revealed there is a complex regulatory relationship between the newly identified lncRNAs and their potential target molecules: mi RNAs,m RNAs.Based on bioinformatics technology,GO functional enrichment and KEGG pathway analysis were performed on potential target genes of the newly identified lncRNAs.The results indicated that lncRNAs that are differentially expressed during anagen andtelogen may directly or indirectly regulate potential target genes.In addition,lnc RNA-HOTAIR transcript was isolated and identified from SHFs of Liaoning cashmere goat.Also,we analyzed its transcriptional pattern and methylation level of HOTAIR gene promoter in SHFs during anagen and telogen.Nucleotide composition analysis showed that the content of Adenine(A)and Thymine(T)was higher than that of Guanine(G)and Cytosine(C)in lnc RNA-HOTAIR transcript of Liaoning cashmere goat SHFs with the highest frequency distribution of AG nucleotide pair(8.06%).The ce RNA regulatory network shows that there is a direct or indirect complex regulatory relationship between lnc RNA-HOTAIR and its potential target molecules: mi RNAs,m RNAs and proteins.Also,transcriptional pattern studied found that the expression of lnc RNA-HOTAIR transcript in anagen SHFs was significantly higher than that in the telogen,which indicated that lnc RNA-HOTAIR transcript may be involved in the regulation of cashmere fiber growth and hair follicle development.The promoter methylation analysis of HOTAIR gene showed that the promoter methylation of HOTAIR gene most likely was involved in the transcriptional suppression of cashmere goat SHFs.To sum up,this study investigated the potential functions and regulatory characteristics of newly identified lncRNAs and lnc RNA-HOTAIR transcripts in SHFs of Liaoning cashmere goat.It provides a theoretical basis for further elucidating that non-coding transcripts are involved in the regulation of SHFs in Liaoning cashmere goat,and also provides a scientific basis for the molecular selective breeding of high-quality cashmere goats.