Nucleic Acids Research Advance Access published online on October 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm742
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Molecular Biology |
Allele-specific demethylation at an imprinted mammalian promoter
1Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, SE1 9RT, UK, 2INSERM U741, Institut Jacques Monod, 2 Place Jussieu, 75251 Paris, CEDEX 05, France and 3Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY10032, USA
* To whom correspondence should be addressed. Tel: +44 (0)207 1883711; Fax: +44(0)207 188 2585; Email: rebecca.oakey{at}genetics.kcl.ac.uk
Received July 4, 2007. Revised August 24, 2007. Accepted September 6, 2007.
A screen for imprinted genes on mouse Chromosome 7 recently identified Inpp5f_v2, a paternally expressed retrogene lying within an intron of Inpp5f. Here, we identify a novel paternally expressed variant of the Inpp5f gene (Inpp5f_v3) that shows a number of unusual features. Inpp5f_v3 initiates from a CpG-rich repeat region adjoining two B1 elements, despite previous reports that SINEs are generally excluded from imprinted promoters. Accordingly, we find that the Inpp5f_v3 promoter acquires methylation around the time of implantation, when many repeat families undergo de novo epigenetic silencing. Methylation is then lost specifically on the paternally derived allele during the latter stages of embryonic development, resulting in imprinted transcriptional activation on the demethylated allele. Methylation analyses in embryos lacking maternal methylation imprints suggest that the primary imprinting mark resides within an intronic CpG island 
1 kb downstream of the Inpp5f_v3 transcriptional start site. These data support the hypothesis that SINEs can influence gene expression by attracting de novo methylation during development, a property likely to explain their exclusion from other imprinted promoters.