Mark Shannon, Linda Ashworth, Jane Lamerdin, Loren Hauser, Elbert Branscomb and Lisa Stubbs
Biology Division, Oak Ridge National Laboratory, P.O. Box 2009, Oak Ridge, TN 37831-8080
As part of a comprehensive man-mouse comparative mapping study of human chromosome 19 being conducted as a collaboration between the Biology Division at the Oak Ridge National Laboratory and the Human Genome Center at the Lawrence Livermore National Laboratory, we have previously identified a conserved cluster of Kruppel-type zinc-finger (ZNF) genes distal to XRCC1 in 19q13.2 and the syntenically homologous region of mouse chromosome 7. Here we report current findings from an ongoing study of the structure, function, and evolution of this apparently homologous pair of gene clusters. Our results indicate that each cluster consists of at least ten related Kruppel-associated box (KRAB)-containing ZNF genes and that the human genes are arranged in tandem over a distance of 350-450kb. We have also found that the KRAB A domains associated with the mouse and human XRCC1-linked ZNF gene clusters are highly similar and are clearly distinct from those of ZNF genes located elsewhere in either genome. Several cDNA clones representing genes in the murine cluster have been isolated using the cluster-identifier 19q13.2 KRAB sequence (hkraba1) as a probe, and three clones have been analyzed in detail. The KRAB A domains of these genes are nearly identical, but other portions of the genes, including the DNA-binding ZNF domains, differ considerably. Interestingly, despite the divergence of ZNF sequences during elaboration of the cluster, Southern analysis suggests that these portions of orthologous mouse and human genes have been remarkably well conserved. Taken together, these data suggest that this cluster of genes may have evolved to encode proteins that recognize different sites in DNA as a result of variant ZNF sequences, while interacting with a common set of transcription factors due to highly similar KRAB domains. Finally, a survey of expression has shown that the mouse genes have highly specific, partially overlapping, but clearly distinct patterns of expression in adult tissues. Transcription factors of the Kruppel-type ZNF subclass presumptively make up nearly 1% of all genes in mammals, are widely found in such contiguous clusters, and are about 16-fold over-represented on human chromosome 19. Our studies open the way for a systematic structural, functional, and evolutionary analysis of these clusters and their constituent genes.
This work was supported by USDOE under contract DE-AC05840R21400 with Lockheed-Martin Energy Systems, Inc., and contract W-7405-ENG-48 with the Lawrence Livermore National Laboratory. M.S. is supported by a DOE Human Genome Distinguished Postdoctoral Fellowship.
 Corresponding author
 Human Genome Center, Lawrence Livermore National Laboratory
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