Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling

Abstract

BackgroundHair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, including DNA methylation, which plays important roles in mammalian cellular identity and is essential for the development of HFs. Secondary hair follicles (SHFs) in cashmere goat exhibit classic cyclic hair development, and little has been done on a genome-wide scale to examine potentially methylated genes involved in the hair cyclic transition.ResultsGenome-wide DNA methylation profiles between skin tissues sampled during the anagen and telogen stages in cashmere goats were investigated using whole-genome bisulfite sequencing (WGBS). The methylation status was observed to be higher in the skin samples with HFs in the telogen than those in the anagen stage. A total of 1311 differentially methylated regions (DMRs) were identified between the two groups, which contained 493 fully annotated DMR-related genes (DMGs) (269 Hyper- DMGs and 224 Hypo-DMGs). Furthermore, a significant over-representation of the functional categories for DMGs related to immune response and intercellular crosstalk during hair cycling was observed. By integrating DNA methylation and mRNA expression data, we revealed that four genes (FMN1, PCOLCE, SPTLC3, and COL5A1) are crucial factors for elucidating epigenetic mechanisms contributing to the telogen-to-anagen transition.ConclusionOur study provided systematic methylome maps pertaining to the hair cycling stages (anagen vs telogen) at a single-base resolution, and revealed stage-specific methylation loci during cashmere growth or quiescence. Furthermore, we identified epigenetically regulated genes that are potentially involved in HF development and growth in cashmere goats, and likely in other mammal species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5002-5) contains supplementary material, which is available to authorized users.

Integrated Analysis of Methylome and Transcriptome Changes Reveals the Underlying Regulatory Signatures Driving Curly Wool Transformation in Chinese Zhongwei Goats

“…While previous studies have determined the effects of selected aspects, such as the genome-wide locus, DNA methylation, transcriptional signatures, and morphology, on the morphogenesis of curly fibers (Hynd et al, 2009;Cheng et al, 2010;Sriwiriyanont et al, 2011;Espada et al, 2014;Fan et al, 2015;Sennett et al, 2015;Gao et al, 2016;Glover et al, 2017;Li et al, 2018;Petridis et al, 2018), a comprehensive study conducting the interplay of genome-wide DNA methylation and transcription synchronously using skin tissues from the same biological replicates in different growth stages had thus far been lacking. The functional regulation of DNA methylation on gene expression has now been established as an effective prospective way to understand the ways that drastic methylation changes relate to hair phenotypic variation (Guo et al, 2014).…”

“…Some critical signaling pathways, including the wingless-related integration site (WNT), ectodysplasin A receptor (EDAR), and bone morphogenetic proteins (BMP) pathways, are regarded as regulatory hubs during fiber development (Lu et al, 2016;Telerman et al, 2017). Mammals, and in particular, sheep and goats have obvious periodic fiber growth with seasonal changes, and the regulatory mechanisms of these changes have been explored in transcriptome studies (Yang et al, 2017;Li et al, 2018). Subsequently, some genetic factors, such as those of the TCHH, KRT gene families, and the metallothionein 3 isoforms, which are related to curly wool, h a v e b e e n d e t e r m i n e d b y R N A -s e q a n a l y s i s a n d immunohistochemical analyses of the fiber proteins (Sriwiriyanont et al, 2011;Yu et al, 2011;Kang et al, 2013).…”

DNA methylation pattern of the goat <i>PITX1</i> gene and its effects on milk performance

“…Y. revealed 10 DMRrelated genes (DMGs) by analyzing the sequencing results of Hu sheep ovaries, which were likely related to the prolificacy of Hu sheep. Li et al (2018) identified potential DMRs and DMGs that were involved in hair follicle development and growth in cashmere goats. Dechow and Liu (2018) detected the DNA methylation patterns in peripheral blood mononuclear cells of Holstein cattle with variable milk yield, and revealed some potential epigenetic variation related to milk performance.…”

Thymosin β4 Identified by Transcriptomic Analysis from HF Anagen to Telogen Promotes Proliferation of SHF-DPCs in Albas Cashmere Goat

“…Cashmere is an important economic product worldwide and the world market for cashmere is increasing, but the current production of cashmere is limited [1][2][3][4]. Albas cashmere goat, famous across the world for its high-quality cashmere, is one of the most precious genetic resources on the Inner Mongolia Plateau in China [5][6][7].…”

“…Due to their important role in cashmere growth, SHF-DPCs serve as an excellent model to investigate the function mechanism of genes on HF in cashmere goats [19][20][21][22]. Therefore, to improve the individual cashmere production of cashmere goats, researchers tried to find the major genes and pathways that may affect the growth and development of SHF-DPCs and HF cycle by transcriptomics and bioinformatics methods [4,12,23].…”