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

Abstract

The Zhongwei goat is kept primarily for its beautiful white, curly pelt that appears when the kid is approximately 1 month old; however, this representative phenotype often changes to a less curly phenotype during postnatal development in a process that may be mediated by multiple molecular signals. DNA methylation plays important roles in mammalian cellular processes and is essential for the initiation of hair follicle (HF) development. Here, we sought to investigate the effects of genome-wide DNA methylation by combining expression profiles of the underlying curly fleece dynamics. Genome-wide DNA methylation maps and transcriptomes of skin tissues collected from 45-to 108-day-old goats were used for whole-genome bisulfite sequencing (WGBS) and RNA sequencing, respectively. Between the two developmental stages, 1,250 of 3,379 differentially methylated regions (DMRs) were annotated in differentially methylated genes (DMGs), and these regions were mainly related to intercellular communication and the cytoskeleton. Integrated analysis of the methylome and transcriptome data led to the identification of 14 overlapping genes that encode crucial factors for wool fiber development through epigenetic mechanisms. Furthermore, a functional study using human hair inner root sheath cells (HHIRSCs) revealed that, one of the overlapping genes, platelet-derived growth factor C (PDGFC) had a significant effect on the messenger RNA expression of several key HF-related genes that promote cell migration and proliferation. Our study presents an unprecedented analysis that was used to explore the enigma of fleece morphological changes by combining methylome maps and transcriptional expression, and these data revealed stage-specific epigenetic changes that potentially affect fiber development. Furthermore, our functional study highlights a possible role for the overlapping gene PDGFC in HF cell growth, which may be a predictable biomarker for fur goat selection.

Expression Profiling and Functional Characterization of miR-26a and miR-130a in Regulating Zhongwei Goat Hair Development via the TGF-β/SMAD Pathway

“…We selected two of the 12 candidate DE miRNAs that exhibited extremely significant differences and predicted their target genes. The predicted miRNA target genes were combined with published transcriptomic analysis data from our lab [ 21 ], to construct a mRNA- and miRNA network related to hair bending. Taking the intersection of the results obtained from the two prediction sites, we found that miR-26a has 667 target genes and miR-130a has 184 target genes.…”

Integrative Analysis of Methylome and Transcriptome Reveals the Regulatory Mechanisms of Hair Follicle Morphogenesis in Cashmere Goat

“…CEBPB, GATA3, and HOXA5, were under the control of DNA methylation and involved in skin and hair follicle differentiation [28]. Through integrated analysis of the methylome and transcriptome, Xiao found 14 crucial factors for wool fiber development under the control of epigenetic mechanisms during curly fleece dynamics in Zhongwei goats [29]. Li revealed that FMN1, PCOLCE, SPTLC3, and COL5A1 were crucial factors for elucidating the epigenetic mechanisms contributing to the telogen-to-anagen transition in cashmere goats [30].…”

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

“…Promoter methylation of HOTAIR gene and related suppressed expression were found to regulate the reconstruction of secondary hair follicles in cashmere goat ( Jiao et al, 2019 ). Furthermore, crucial regulatory roles for DNA methylation in wool fiber development and transformation of fur with special characters and production purpose, such as curly wool with beautiful white color or high-quality brush hair, have been observed ( Qiang et al, 2018 ; Xiao et al, 2019 ).…”