Discovery of a Novel, Paternally Expressed Ubiquitin-specific Processing Protease Gene through Comparative Analysis of an Imprinted Region of Mouse Chromosome 7 and Human Chromosome 19q13.4

Although the two alleles of most mammalian autosomal genes are functionally equivalent, the maternal and paternal copies of a subset of genes are distinguished by genomic imprinting, a mechanism by which one allele is epigenetically modified and repressed, depending upon parental origin. The epigenetic modification that determines imprinting is yet to be defined, but several lines of evidence strongly suggest that differences in DNA methylation and chromatin structure may be part of the molecular mechanism (Tilghman 1999). About 30 different imprinted genes have been isolated from human and mouse DNA, and more imprinted genes are predicted to be present in mammalian genomes (Barlow 1997; Morrison and Reeve 1998). The imprinted genes that have been described to date are clustered in discrete chromosomal regions, and the clustering of those genes is conserved in mammals (Barlow 1995; Bartolomei and Tilghman 1997). These data have been interpreted to imply that genome imprinting is a long-range mechanism that controls allele-specific transcription of multiple genes within a defined chromosomal region (Nicholls 1994; Dittrich et al. 1996; Tilghman et al. 1998, 1999). Imprinted genes exhibit several unique features in addition to parent-of-origin-specific monoallelic expression and differential methylation. The known imprinted genes generally are expressed at early stages of development, and many encode proteins with functions related to embryonic growth (Tilghman 1999). Recent studies also suggest the involvement of imprinted genes in controlling the parental caring behavior of mammals (Lefebvre et al. 1998; Li et al. 1999). Several imprinted genes such as UBE3A (Rougeulle et al. 1998), IGF2 (Moore et al. 1997), ZNF127 (Jong et al. 1999), and IGF2R (Wutz et al. 1997) display bidirectional transcription, producing both sense and antisense transcripts. A number of imprinted genes including H19 and IPW are expressed without any coding capability; the final products of these genes are RNAs rather than proteins (Bartolomei and Tilghman 1997). Imprinted genes also tend to be comosed of relatively small numbers of exons and to contain smaller introns than nonimprinted genes (Hurst et al. 1996), although there are some notable exceptions (e.g., KvLQT1; Lee et al. 1997). Early mouse genetic studies with translocation mutant mice predicted the presence of nine different imprinted domains distributed onto seven chromosomes (Beechey and Cattanach 1996). The chromosomal locations of most imprinted genes, in fact, are consistent with this initial prediction (Imprinting Map; http://www.mgu.har.mrc.ac.uk/imprinting/imptables.html#impmaps). Mouse chromosome 7 (Mmu7) was predicted in these early studies to contain three different imprinted domains, located in centromeric, central, and distal regions (Searle and Beechey 1990). The central and distal regions of Mmu7 are syntenically homologous to intervals of human chromosome 15q13-11 and 11p15, respectively, that contain genes associated with two imprinting genetic disorders—Prader–Willi/Angelman (Nicholls et al. 1998) and Beckwith–Wiedemann syndromes (Reik and Maher 1997). Each of these domains contains several imprinted genes whose order, sequence, and imprinting status are highly conserved in humans and mice. Until recently, only one imprinted gene, Peg3 (paternally expressed gene 3), had been localized to the centromeric imprinted domain of Mmu7 (Kuroiwa et al. 1996) and the homologous region of human chromosome 19q13.4 (Kim et al. 1997a). We exploited the well-developed physical map surrounding human PEG3 and the known conservation of this interval in humans and mice to identify a second mouse-imprinted gene, Zim1 (imprinted zinc-finger gene 1), located downstream of Peg3 (Kim et al. 1999). More recent studies identified a related and homologously positioned human zinc-finger gene, ZIM2, and showed that the gene shares seven 5′-exons with PEG3, a feature that distinguishes this pair of human genes from their closest murine counterparts (Kim et al. 2000). The significant divergence of Zim1 and ZIM2 gene organization and amino acid sequence suggests that the region surrounding PEG3 has undergone significant changes during the course of mammalian evolution. Through analysis of clone contigs spanning homologous segments of Mmu7 and sequenced regions of human 19q13.4, we have isolated and characterized another novel mouse gene, Usp29 (ubiquitin-specific processing protease 29) and have identified its human counterpart. Our analyses show that Usp29 is also imprinted and is expressed mainly from the paternal allele during embryogenesis and in adult brain. The sequence of a full-length 7.6-kb mouse cDNA clone and human coding sequences indicate that Usp29 encodes a novel ubiquitin-specific processing protease, and together with Ube3a may represent a second imprinted gene involved in the ubiquitination pathway.