A Small Family of Sushi-Class Retrotransposon-Derived Genes in Mammals and Their Relation to Genomic Imprinting Neil A. Youngson, Sylvia Kocialkowski, Nina Peel, Anne C. Ferguson-Smith Department of Anatomy, University of Cambridge, Downing St, Cambridge CB23DY, UK Received: 19 November 2004 / Accepted: 29 March 2005 [Reviewing Editor: Dr. Juergen Brosius] Abstract. Ty3/gypsy retrotransposons are rare in mammalian genomes despite their abundance in invertebrate and other vertebrate classes. Here we identify a family of nine conserved mammalian genes with homology to Ty3/gypsy retrotransposons but which have lost their ability to autonomously retro- transpose. Of these, five map to the X chromosome while the remaining four are autosomal. Comparative phylogenetic analyses show them to have strongest homologytothesushi-ichielementfrom Fugu rubripes. Two of the autosomal gene members, Peg10 and Rtl1, are known to be imprinted, being expressed from the paternally inherited chromosome homologue. This suggests, consistent with the host-parasite response theory of the evolution of the imprinting mechanism, that parental-origin specific epigenetic control may be mediated by genomic ‘‘parasitic’’ elements such as these. Alternatively, these elements may preferentially integrate into regions that are differentially modified on the two homologous chromosomes such as im- printed domains and the X chromosome and acquire monoallelic expression. We assess the imprinting sta- tus of the remaining autosomal members of this family and show them to be biallelically expressed in embryo and placenta. Furthermore, the methylation status of Rtl1 was assayed throughout development and was found to resemble that of actively, silenced repetitive elements rather than imprinted sequences. This indi- cates that the ability to undergo genomic imprinting is not an inherent property of all members of this family of retroelements. Nonetheless, the conservation but functional divergence between the different members suggests that they have undergone positive selection and acquired distinct endogenous functions within their mammalian hosts. Key words: LTR retrotransposon — Genomic imprinting — Ty3-gypsy — Mammalian — Sushi-ichi — Bisulphite sequencing — CpG methylation Introduction More than 45% of the human genome is derived from repetitive parasitic elements such as transposons, retrotransposons, and retroviruses (Lander et al. 2001). These elements can be detrimental to the host and multiple strategies in different organisms have been utilized to combat this, many involving epige- netic mechanisms (Yoder et al. 1997; Birchler et al. 2000; Matzke et al. 2002). In mammalian genomes, these elements are generally silenced by mechanisms involving cytosine methylation. DNA methylation is also involved in genomic imprinting, a process that causes a subset of genes to be expressed in a parental- origin specific manner. Certain classes of a repetitive parasitic element appear to be methylated in a parental-origin specific manner in the gametes (Rubin et al. 1984; Sanford et al. 1987; Chesnokov and Schmid, 1995; Lane et al. 2003). Hence, a relationship between this and the evolution of the imprinting mechanism has been suggested (Barlow, 1993). The The sequence data from this study have been submitted to Entrez/ NCBI under accession nos. BN000778 to BN000783. Correspondence to: A. C. Ferguson-Smith; email: afsmith@ mole.bio.cam.ac.uk J Mol Evol (2005) 61:481–490 DOI: 10.1007/s00239-004-0332-0