Identification and characterization of methylation-dependent/independent DNA regulatory elements in the human SLC9B1 gene

• The full-length NHEDC1 protein expression is restricted to human testes.
• Two putative promoters (P1 and P2) and two CpG islands were found in the hNHEDC1 gene.
• P1 and CpGI overlap and display methylation-dependent promoter activity.
• P1/CpGI is hypomethylated in human testes and hypermethylated in lung.
• CpGII displays promoter, cell type, and methylation dependent regulatory activity.

The human NHEDC1 (hNHEDC1) protein is thought to be essential for sperm motility and fertility however the mechanisms regulating its gene expression are largely unknown. In this study we have identified multiple DNA regulatory elements in the 5ʹ end of the gene encoding hNHEDC1 (SLC9B1) and have explored the role that DNA methylation at these elements plays in the regulation of its expression. We first show that the full-length hNHEDC1 protein is testis-specific for the tissues that we tested and that it localizes to the cells of the seminiferous tubules. In silico analysis of the SLC9B1 gene locus identified two putative promoters (P1 and P2) and two CpG islands – CpGI (overlapping with P1) and CpGII (intragenic) – at the 5ʹ end of the gene. By deletion analysis of P1, we show that the region from − 23 bp to + 200 bp relative to the transcription start site (TSS) is sufficient for optimal promoter activity in a germ cell line. Additionally, in vitro methylation of the P1 (the − 500 bp to + 200 bp region relative to the TSS) abolishes its activity in germ cells and somatic cells strongly suggesting that DNA methylation at this promoter could regulate SLC9B1 expression. Furthermore, bisulfite-sequencing analysis of the P1/CpGI uncovered reduced methylation in the testis vs. lung whereas CpGII displayed no differences in methylation between these two tissues. Additionally, treatment of HEK 293 cells with 5-aza-2-Deoxycytidine led to upregulation of NHEDC1 transcript and reduced methylation in the promoter CpGI. Finally, we have uncovered both enhancer and silencer functions of the intragenic SLC9B1 CpGII. In all, our data suggests that SLC9B1 gene expression could be regulated via a concerted action of DNA methylation-dependent and independent mechanisms mediated by these multiple DNA regulatory elements.

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