Integrative analysis reveals ncRNA-mediated molecular regulatory network driving secondary hair follicle regression in cashmere goats

Abstract

BackgroundCashmere is a keratinized product derived from the secondary hair follicles (SHFs) of cashmere goat skins. The cashmere fiber stops growing following the transition from the actively proliferating anagen stage to the apoptosis-driven catagen stage. However, little is known regarding the molecular mechanisms responsible for the occurrence of apoptosis in SHFs, especially as pertains to the role of non-coding RNAs (ncRNAs) and their interactions with other molecules. Hair follicle (HF) degeneration is caused by localized apoptosis in the skin, while anti-apoptosis pathways may coexist in adjacent HFs. Thus, elucidating the molecular interactions responsible for apoptosis and anti-apoptosis in the skin will provide insights into HF regression.ResultsWe used multiple-omics approaches to systematically identify long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs expressed in cashmere goat skins in two crucial phases (catagen vs. anagen) of HF growth. Skin samples were collected from three cashmere goats at the anagen (September) and catagen (February) stages, and six lncRNA libraries and six miRNA libraries were constructed for further analysis. We identified 1122 known and 403 novel lncRNAs in the goat skins, 173 of which were differentially expressed between the anagen and catagen stages. We further identified 3500 gene-encoding transcripts that were differentially expressed between these two phases. We also identified 411 known miRNAs and 307 novel miRNAs, including 72 differentially expressed miRNAs. We further investigated the target genes of lncRNAs via both cis- and trans-regulation during HF growth. Our data suggest that lncRNAs and miRNAs act synergistically in the HF growth transition, and the catagen inducer factors (TGFβ1 and BDNF) were regulated by miR-873 and lnc108635596 in the lncRNA-miRNA-mRNA networks.ConclusionThis study enriches the repertoire of ncRNAs in goats and other mammals, and contributes to a better understanding of the molecular mechanisms of ncRNAs involved in the regulation of HF growth and regression in goats and other hair-producing species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4603-3) contains supplementary material, which is available to authorized users.

CircRNA-1926 Promotes the Differentiation of Goat SHF Stem Cells into Hair Follicle Lineage by miR-148a/b-3p/CDK19 Axis

“…The circRNA-1926 is 3887-nt in length, and it exhibited significantly higher level at anagen than the counterpart at telogen [16]. The potential miRNA target sites within circRNA-1926 were predicted and screened through taking intersection of the analysis of three programs: miRDB, RNAhybrid, and miRNA-target, as described in our previous study [1]. We performed the analysis on the nucleotide composition and frequency distribution of nucleotide pairs with MEGA program (Version 6.0) [17].…”

“…Cashmere is precious natural protein fiber derived from cashmere goats, and its textiles have been favored by consumers due to their typical features, like fine, light, softness, and comfort [1,2]. In cashmere goats, the cashmere growth is controlled by biological cycles of secondary hair follicle (SHF) consisting of anagen, catagen, and telogen [3].…”

Cultivation of Hair Matrix Cells from Cashmere Goat Skins and Exemplified Applications

“…Concurrent with HFs’ yearly sequential switching from growth stage (anagen), regression stage (catagen), and resting stage (telogen), the cashmere annually elongates and sheds [ 2 , 3 ]. In early efforts to delineate molecular mechanisms governing the dynamic transitions of HFs among these stages and seasonal cashmere regrowth, a large quantity of protein-coding and non-protein-coding transcripts [ 4 , 5 ], as well as several epigenetic modifications on genomic and post-transcriptional levels [ 6 , 7 ], have been filtered as potential participators via utilizing high-throughput-based sequencing strategies, such as RNA-seq. For instance, we previously performed a comprehensive transcript profiling of goat skin tissues at anagen and catagen, then simultaneously identified a total of 3500 mRNAs, 72 microRNAs (miRNAs), and 173 long noncoding RNAs (lncRNAs) that are differentially expressed between the two stages, hinting that the anagen-to-catagen transition may be under the guidance of an intricate network constituted by numerous lines of interacting coding and noncoding genes [ 5 ].…”

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)

“…Although there were only three pathways in which the sulfur relay system, sulfur metabolism, and glycosaminoglycan degradation were found to be significantly enriched, the host genes of circRNA6854 and circRNA815 were involved in all pathways. Studies have shown that intermediate filaments are probably the key factors involved in cashmere growth 34 . In addition, several important pathways that play a role in dominating hair follicle development were reported, such as the PPAR pathway 35 , Wnt signaling pathway 5,36,37 , MAPK signaling pathway 38 , and NF-kappa B signaling pathway 39 .…”