Comparative sequence analysis of the imprinted Dlk1-Gtl2 locus in three mammalian species reveals highly conserved genomic elements and refines comparison with the Igf2-H19 region

The Dlk1-Gtl2 domain on Mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common feat ures involved in imprinting control. We have sequenced this conserved regio n in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and ident ification of highly conserved sequence elements, some of which we have show n previously to be differentially methylated in the mouse. Additionally, th is analysis facilitated identification of a CpG-rich tandem repeat array lo cated similar to 13-15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the Mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extended Dlk1 transcripts. Because Dlk1 and Gtl2 share many of the imprinting properties of the well-characterized Igf2-H19 domain, it has been proposed that the two regions may be regulated in the s ame way. Comparative genomic examination of the two domains indicates that although there are similarities, other features are very different, includi ng the location of conserved CTCF-binding sites, and the level of conservat ion at regulatory regions.