DNA methylation plays a critical role in early embryonic skin development by controlling gene expression. Act as an indirect regulator, long non-coding RNA (lncRNA) recruit DNA methyltransferases to specific genomic sites to methylate DNA. However, the molecular regulation mechanisms underlying hair follicle morphogenesis is unclear in cashmere goat. In this study, RNA-seq and Whole-genome bisulfite sequencing (WGBS) in embryonic day 65 (E65) and E120 skin tissues of cashmere goat were used to reveal this complex regulatory process. RNA-seq, qRT-PCR and immunohistochemistry results showed that Wnt signaling played an important role in both hair follicle induction and differentiation stage, transcriptional factors (TFs) including Hoxc13, Sox9, Sox21, Junb, Lhx2, Vdr and Gata3 participated in hair follicle differentiation via specific expression at E120. Subsequently, combination of WGBS and RNA-seq analysis showed that the expression of hair follicle differentiation genes and TFs genes was negatively correlated with DNA methylation level generally. A portion of hair follicle differentiation genes were methylated and repressed in hair follicle induction stage but were subsequently demethylated and expressed during hair follicle differentiation stage, suggesting DNA methylation play an important role in hair morphogenesis through regulating associated gene expression. Furthermore, the potential differentially expressed lncRNAs associated with DNA methylation on target gene were revealed. LncRNA XR_001918556 may affect the DNA methylation of TFs gene Gata3, lnc-003786 may affect the DNA methylation of signaling gene Fgfr2. In conclusion, differentiation genes were governed by DNA methylation, resulting in repressed expression in hair follicle induction stage and high expression in hair follicle differentiation stage. Furtherly, potential lncRNAs associated with DNA methylation on target genes were delineated. This study would enrich the regulatory network and molecular mechanisms on hair morphogenesis.
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