|Functional Genomics Section
DOE Human Genome Program Contractor-Grantee Workshop
132. Comparative Analysis of Structure and Function in an Imprinted Region of Proximal Mouse Chromosome 7 and the Related Region of Human Chromosome 19q13.4
Joomyeong Kim, Anne Bergmann, Xiaochen
Lu, Anne Olsen, Jane Lamerdin, and Lisa Stubbs
Our group is interested in coupling mouse genetics and biology to comparative sequence that is being generated by JGI teams, with the aim of generating in-depth functional annotation the sequenced human regions. One special target for these studies has been a 2 Mb-region of human chromosome 19q13.4 (H19q13.4) and the syntenically homologous region of mouse chromosome 7 (Mmu7). The sequence of the human region is nearly completed by the JGI genome sequencing team, and sequence analysis of the homologous murine has recently been initiated. Since the murine region is known to be parentally imprinted and imprinting is a generally conserved in mammalian species, the structure and function of this region are of special biological interest.
Our group's efforts begin as DNA sequence and basic annotation of specific DNA segments are completed. Our goal is to characterize genes and conserved regulatory sequences predicted to exist in the sequenced regions, especially those that may contribute to parent-of-origin specific functions in humans and mice . The human region is especially rich in clustered zinc finger containing genes (ZNFs); about 90% of the genes found in 19q13.4 appear to be actively expressed Kruppel-type ZNF loci. We have also identified a number of other types of genes in the 2 Mb human interval, including genes encoding an Aurora-related serine/threonine kinase (STK13), a sulfotransferase2 (ST2), and one anonymous gene homologous to a yeast hypothetical protein P38334 (HYP). The mouse region is similar in terms of gene content, but physical mapping studies have also revealed several chromosomal changes that are unique to the mouse. For example, there are at least 5 copies of the STK13-related genes in mouse, and these copies appear to have been duplicated in tandem as part of a large unit that also contains ZNF-related gene sequences. This tandem duplication appears to have occurred in very recent evolutionary history. One gene (Cln4-2), whose homolog is located in the pseudoautsomal region of the human X chromosome and which had previously been mapped to Mmu7, also appears to have been very recently transposed into the mouse zinc-finger gene cluster region. Other orthologs of human 19q13.4 genes, including ST2, and HYP are present in the related mouse region, although their relative positions within the mouse and human regions have not been strictly conserved. The intronless nature of many of these genes suggests that they were duplicated by retroposition and inserted into this region after the zinc-finger gene clusters were elaborated.
Detailed functional studies have been focused primarily on the imprinted genes that are located in this region. Only one imprinted gene, paternally expressed gene 3 (Peg3) had been identified at the outset of this study, but we have recently identified several new genes located near Peg3. At least one of the new genes, called Zim1, is also imprinted in mouse. Peg3 and Zim1 are located next to each other in both species, and the two genes are reciprocally-imprinted: Peg3 is paternally expressed whereas Zim1 is expressed only from the maternal allele and specifically in embryonic tissues. As has been found in other well-known imprinted domains, such as Prader-Willi/ Angelman syndrome region of H15q11-q13/Mmu7 and Beckwith-Wiedemann region of H11p15.5/Mmu7, the H19q13.4/proximal Mmu7 imprinted domain is expected to contain a number of additional imprinted genes. A comprehensive update on our recent studies, including gene identification, gene expression, and functional analysis of this gene-rich, imprinted region will be presented.
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