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Background  Two evolutionarily Conserved Sequence Elements, CSE1 and CSE2 (YY1 binding sites), are found within the 3.8-kb CpG island surrounding the bidirectional promoter of two imprinted genes,  Peg3  (Paternally expressed gene 3) and  Usp29  (Ubiquitin-specific protease 29). This CpG island is a likely ICR (Imprinting Control Region) that controls transcription of the 500-kb genomic region of the  Peg3  imprinted domain.    Results  The current study investigated the functional roles of CSE1 and CSE2 in the transcriptional control of the two genes,  Peg3  and  Usp29 , using cell line-based promoter assays. The mutation of 6 YY1 binding sites (CSE2) reduced the transcriptional activity of the bidirectional promoter in the  Peg3  direction in an orientation-dependent manner, suggesting an activator role for CSE2 (YY1 binding sites). However, the activity in the  Usp29  direction was not detectable regardless of the presence/absence of YY1 binding sites. In contrast, mutation of CSE1 increased the transcriptional activity of the promoter in both the  Peg3  and  Usp29  directions, suggesting a potential repressor role for CSE1. The observed repression by CSE1 was also orientation-dependent. Serial mutational analyses further narrowed down two separate 6-bp-long regions within the 42-bp-long CSE1 which are individually responsible for the repression of  Peg3  and  Usp29 .    Conclusion  CSE2 (YY1 binding sites) functions as an activator for  Peg3  transcription, while CSE1 acts as a repressor for the transcription of both  Peg3  and  Usp29 .

Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription