Inner Mongolian cashmere goats (IMCGs) are well-known for excellent cashmere quality, and are famous cashmere and meat goat breeds in China. IMCGs coat hair types (HTs) are mainly divided into two types, including long hair type (LHT) and short hair type (SHT). Cashmere fineness and quality are significant different between the two HTs. Hair follicles are essential to villi growth and are closely related to different HTs. However, epigenetic mechanism of hair follicle growth in different HTs is not fully understood. In this study, IMCGs were selected to explore potential regulatory relationship between differentially expressed genes and chromatin accessibility, histone modification and DNA methylation status through comprehensive analysis of ATAC-seq, CUT&Tag and WGBS data of skin tissue.
 As transcriptome of two HTs were most significantly different in telogen, this period of hair follicles were selected in further analyses. ATAC-seq and CUT&Tag results showed that the open chromatin region was more abundant in LHT skin. 3,096 up-regulated chromatin accessibility peaks and 1,388 down-regulated chromatin accessibility peaks were discovered between two HTs. Histone H3K4me3 and H3K27ac modifications were mainly enriched in genes transcription start site (TSS) region, and there were 1,917 different H3K4me3 modification genes and 1,699 different H3K27ac modification genes between two HTs. PDGFC, ITGA5, PAK1, BCL2 and VAV3 had significant differences in open chromatin region and histone modification of H3K4me3 and H3K27ac. During the growth of hair follicles in LHT, PDGFC showed more open chromatin areas, and modification of histone H3K27ac was relatively high. H3K4me3 modification of VAV3 was also highly enriched in hair follicles of LHT. These differential genes were significantly enriched in PI3K-Akt, Ras, Rap1 and other signaling pathways. With WGBS, VAV3 gene was hypermethylated and the PDGFC gene was hypomethylated in hair follicles of LHT. These differential regulated genes were mainly enriched in Rap1, MAPK and cAMP signaling pathways, which were all closely related to periodic growth of hair follicles. Therefore, this study suggests that PDGFC and VAV3 may be regulated by open chromatin status, histone modification, and DNA methylation, and further affect hair follicle growth of different HTs through Rap1 and MAPK signaling pathways. This study provides a new perspective on the transcriptional regulation mechanism of hair follicle growth differences in IMCGs with different HTs, and provides a theoretical basis for improving quality and production of cashmere.
 

coat types,epigenetics,histone modification,inner mongolian cashmere goats