Table_4_Integrated Analysis of Methylome and Transcriptome Changes Reveals the Underlying Regulatory Signatures Driving Curly Wool Transformation in Chinese Zhongwei Goats.xlsx

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.

中卫山羊（Zhongwei goat）主要因其约1月龄羔羊所产出的洁白卷曲裘皮而被饲养，但这一典型表型在产后发育过程中常会逐渐变为卷曲度更低的表型，该过程或受多种分子信号介导。DNA甲基化（DNA methylation）在哺乳动物细胞进程中发挥关键作用，且对毛囊（hair follicle, HF）发育的启动不可或缺。本研究旨在结合卷曲裘皮动态变化的表达谱，探究全基因组DNA甲基化的调控效应。研究采集了45日龄至108日龄山羊的皮肤组织，分别通过全基因组亚硫酸氢盐测序（whole-genome bisulfite sequencing, WGBS）与RNA测序构建全基因组DNA甲基化图谱及转录组。在两个发育阶段间，3379个差异甲基化区域（differentially methylated regions, DMRs）中有1250个被注释至差异甲基化基因（differentially methylated genes, DMGs），此类区域主要与细胞间通讯及细胞骨架相关。通过整合甲基化组与转录组数据进行分析，本研究鉴定出14个重叠基因，这些基因可通过表观遗传机制调控羊毛纤维发育，发挥关键作用。进一步利用人毛囊内根鞘细胞（human hair inner root sheath cells, HHIRSCs）开展功能实验，结果显示其中一个重叠基因——血小板衍生生长因子C（platelet-derived growth factor C, PDGFC）——可显著影响若干促进细胞迁移与增殖的关键毛囊相关基因的信使RNA（messenger RNA, mRNA）表达水平。本研究首次结合甲基化组图谱与转录表达谱解析裘皮形态变化的奥秘，揭示了可能影响纤维发育的阶段特异性表观遗传改变。此外，本研究的功能实验证实重叠基因PDGFC在毛囊细胞生长中具有潜在调控作用，有望成为裘皮山羊选育的可预测性生物标志物。