Abstract. The Sry (sex determining region on Y chromosome) gene is a master gene for sex determination. We previously reported that the Sry gene has tissue-dependent and differentially methylated regions (T-DMRs) by analyzing the DNA methylation states at CpG sites in the promoter regions. In this study, we found unique non-CpG methylation at the internal cytosine in the 5'-CCTGG-3' pentanucleotide sequence in the Sry T-DMR. This non-CpG methylation was detected in four mouse strains (ICR, BALB/c, DBA2 and C3H), but not in two strains (C57BL/6 and 129S1), suggesting that the CCTGG methylation is tentative and unstable. Interestingly, this CCTGG methylation was associated with demethylation of the CpG sites in the Sry T-DMR in the developmental process. A methylationmediated promoter assay showed that the CCTGG methylation promotes gene expression. Our finding shows that non-CpG methylation has unique characteristic and is still conserved in mammals. Key words: DNA methylation, Non-CpG methylation, Sry (J. Reprod. Dev. 57: [586][587][588][589][590][591][592][593] 2011) NA methylation plays an important role in normal differentiation, development and cloned animals [1][2][3][4]. Eukaryotic DNA contains 5-methylcytosine as the only methylated nucleotide in the genome. The methylation of cytosine occurs mainly at the CpG site in mammals [5][6][7]. Non-CpG methylation in mammals is quite rare, whereas non-CpG methylation as CNG (N can be any base) is common in plants [8], bacteria [9,10] and yeast [11]. In mammals, DNA methylation of CpGs is involved in various phenomena from development through gene silencing, splicing, stabilizing and chromatin remodeling [1,[12][13][14][15][16][17][18][19][20][21]. In contrast, the biological role of non-CpG methylation in mammals is unknown.Sry (sex determining region on the Y chromosome) is the master gene for initiating the cascade leading to testicular differentiation in mammals [22]. Expression of the Sry gene is restricted to gonadal somatic cells at 10.5-12.5 days postcoitum (dpc) in the mouse [23][24][25]. The Sry gene produces two types of transcripts with different transcription start sites, linear and circular forms [24,26]. The linear transcript is translated into protein and is expressed only from 10.5 to 12.5 dpc in the pre-Sertoli cells in the developing male gonad [23][24][25], whereas the circular form is thought to be untranslated [23,[27][28][29]. The Sry gene has tissue-dependent and differentially methylated regions (T-DMRs), and the CpG methylation kinetics coincide with the spatio-temporal expression of the Sry gene [19]. Thus, the Sry locus may be an interesting model for acquiring the epigenetic regulation and development of the gonad from the evolutional aspect in mammals.Previous studies reported methylation at the CCWGG (W=A or T) pentanucleotide sequence in mammals [30][31][32][33], but the function of CCWGG methylation remains unknown. Here, we report on the methylation of the CCTGG pentanucleotide sequence in the Sry locus. We examined DNA methyla...