A Novel Variant of Inpp5f Is Imprinted in Brain, and Its Expression Is Correlated with Differential Methylation of an Internal CpG Island

Abstract

Using a tissue-specific microarray screen in combination with chromosome anomalies in the mouse, we identified a novel imprinted gene, Inpp5f_v2 on mouse chromosome 7. Characterization of this gene reveals a 3.2-kb transcript that is paternally expressed in the brain. Inpp5f_v2 is a variant of the related 4.7-kb transcript, Inpp5f, an inositol phosphatase gene that is biallelically expressed in the mouse. Inpp5f_v2 uses an alternative transcriptional start site within an intron of Inpp5f and thus has a unique alternative first exon. Whereas other imprinted transcripts have a unique first exon located within intron 1 of a longer transcript variant (such as at the Gnas and WT1 loci), Inpp5f_v2 is the first example of which we are aware in which the alternative first exon of an imprinted gene is embedded in a downstream intron (intron 15) of a transcript variant. The CpG island associated with the nonimprinted Inpp5f gene is hypomethylated on both alleles, a finding consistent with biallelic expression, whereas the CpG island present 5′ of Inpp5f_v2 is differentially methylated on the maternal versus paternal alleles consistent with its imprinting status.

ACKNOWLEDGMENTS

This study was supported by PHS grant GM58759 from the National Institutes of Health (R.J.O.) and by The Wellcome Trust (R.J.O.). J.D.C. is supported by an IRG fellowship from the GKT School of Medicine, King's College London, and A.J.W. is supported by a studentship from the Generation Trust.

We thank Colin V. Beechey for the T65H mouse tissues and careful reading of the manuscript. We thank Kathryn Woodfine for Affymetrix GeneChip hybridizations and Trevelyan Menheniott and Reiner Schulz for analysis of Affymetrix microarray data and statistical analysis.