Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin. We analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g. SPHK1, GHR, PPP1R27, CSRP2, EEF1A2, and PTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans. Our study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans.

中文翻译：

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综合转录组和甲基化组分析描绘了美利奴绵羊毛囊发育和羊毛相关性状的生物学基础

毛囊发育的分子机制表征对于绵羊羊毛相关性状和人类皮肤相关性状的遗传改良至关重要。美利奴羊是世界上最重要的细毛绵羊品种。在这项研究中，我们通过整合来自美利奴绵羊皮的转录组和甲基化组数据集，系统地研究了绵羊毛囊发育的复杂性。我们分析了 72 个序列数据集，包括 DNA 甲基化组和四种基因类型的整个转录组，即蛋白质编码基因 (PCG)、lncRNA、circRNA 和 miRNA，跨越四个胚胎日（E65、E85、E105 和 E135）和两个来自 18 只美利奴羊的皮肤组织的产后天数（P7 和 P30）。我们揭示了这四种基因类型在六个毛囊发育阶段的不同表达谱，并证明了它们与 DNA 甲基化的复杂相互作用。具有阶段特异性表达或受阶段特异性 lncRNA、circRNA 和 miRNA 调控的 PCG 在上皮分化和毛囊形态发生中显着富集。调控网络和基因共表达分析确定了控制毛囊发育的关键转录本。我们进一步预测转录因子（例如 KLF4、LEF1、HOXC13、RBPJ、VDR、RARA 和 STAT3）在毛囊形态发生中具有特定阶段的参与。通过将这些阶段特定的基因组特征与 7135 只美利奴羊的五种羊毛相关性状的全基因组关联研究 (GWAS) 的结果相结合，我们检测到与绵羊羊毛相关性状相关的发育阶段和基因。例如，在 E105 特异性上调的基因与大多数羊毛相关性状显着相关。一项全现象关联研究 (PheWAS) 表明，绵羊中羊毛相关性状（例如 SPHK1、GHR、PPP1R27、CSRP2、EEF1A2 和 PTPN1）的候选基因也与人类的皮肤病学、代谢和免疫特征显着相关。我们的研究为毛囊形态发生的分子基础提供了新的见解，并将作为改善绵羊羊毛性状育种的基础。它还表明研究器官正常发育中的基因表达对于了解牲畜重要经济性状的遗传结构的重要性。