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Background  During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesize large amounts of hair keratin proteins. In this process, HOXC13 is one critical regulatory factor, proved by the hair defects in HOXC13 mutant mice and HOXC13 mutant patients. However, inconsistent conclusions were drawn from previous researches regarding the regulation of HOXC13 on different keratins. Whether HOXC13 has extensive and unified regulatory role on these numerous keratins is unclear.    Results  In this study, firstly, RNA-seq was performed to reveal the molecular mechanism of cashmere cycle including anagen and telogen. Subsequently, combining the sequencing with qRT-PCR and immunofluorescent staining results, we found that  HOXC13  showed similar expression pattern with a large proportion of keratins except for KRT1 and KRT2, which were higher in anagen compared with telogen. Then, the regulatory role of HOXC13 on different keratins was investigated using dual-luciferase reporter system and keratin promoter-GFP system by overexpressing HOXC13 in HEK 293 T cells and dermal papilla cells. Our results demonstrated that HOXC13 up-regulated the promoter activity of  KRT84  and  KRT38 , while down-regulated the promoter activity of  KRT1  and  KRT2 , which suggested HOXC13 had an ambivalent effect on the promoters of different KRTs. Furtherly, the regulation on HOXC13 itself was investigated. At transcriptional level, the binding sites of HOXC13 and LEF1 were found in the promoter of  HOXC13 . Then, through transfecting corresponding overexpression vector and dual-luciferase reporter system into dermal papilla cells, the negative-feedback regulation of HOXC13 itself and positive regulation of LEF1 on  HOXC13  promoter were revealed. In addition, melatonin could significantly increase the promoter activity of  HOXC13  under the concentration of 10 μM and 25 μM by adding exogenous melatonin into dermal papilla cells. At post-transcriptional level, we investigated whether chi-miR-200a could target  HOXC13  through dual-luciferase reporter system. At epigenetic level, we investigated the methylation level of  HOXC13  promoter at different stages including anagen, telogen and 60d of embryonic period. As a result, miR-200a and methylation were not regulatory factors of HOXC13. Interestingly, we found two SNPs (c.812A > G and c.929A > C) in the homeodomain of  HOXC13  that could deprive the regulatory function of HOXC13 on keratins without changing its protein expression.    Conclusion  HOXC13 had an inconsistent effect on the promoters of different keratins. Two SNPs (c.812A > G and c.929A > C) in the homeodomain of HOXC13 deprived its function on keratin regulation. Besides, the negative-feedback regulation by HOXC13 itself and positive regulation by LEF1 and melatonin on  HOXC13  promoter were revealed. This study will enrich the function of HOXC13 on keratin regulation and contribute to understand the mechanism of hair follicle differentiation.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5011-4) contains supplementary material, which is available to authorized users.

The inconsistent regulation of HOXC13 on different keratins and the regulation mechanism on HOXC13 in cashmere goat (Capra hircus)