Lisa Stubbs, Johannah Doyle, Ethan Carver, Karen Rollins, Laura Chittenden, Mark Shannon, Joomyeong Kim, Linda Ashworth[1], and Elbert Branscomb[1]
Biology Division, Oak Ridge National Laboratory, P.O. Box 2009, Oak Ridge, TN 37831-8077.
Numerous studies have confirmed the notion that mouse and human chromosomes resemble each other closely within blocks of syntenic homology that vary in size widely, containing from just a few to several hundred related genes. Within the best-mapped of these homologous regions, the presence and location of specific genes can be accurately predicted in one species, based upon the mapping results obtained in the other. In addition, information regarding gene function derived from the analysis of human hereditary traits or mapped murine mutations, can also be extrapolated from one species to another. However, syntenic relationships are still not established for many human regions, and local rearrangements including apparent deletions, inversions, insertions, and transposition events, complicate most of the syntenically homologous regions that appear simple on the gross genetic level. Because of these complications, the power of prediction afforded in any homology region increases tremendously with the level of resolution and degree of internal consistency associated with a particular set of comparative mapping data. Our groups have been interested in further defining the borders of syntenic linkage groups in human and mouse, and upon devising means of exploiting the relationships between the two genomes for the discovery of new genes and other functional units in both species.
One of the larger contiguous blocks of mouse-human genomic homology includes the proximal portion of mouse chromosome 7 (Mmu7), and all murine homologs of genes mapping to human chromosome l9q (H19q) that have been recorded to date. Detailed analysis of this large region of mouse-human homology have served as the initial focus of these collaborative studies. Our results have shown that gene content, order and spacing are remarkably well-conserved throughout the length of this approximately 23 cM/29 Mb region of mouse-human homology, except for (1) an overall "inversion" of sequences relative to the centromere, (2) three apparent "transpositions" of gene-rich segments in mouse relative to man, and (3) two inversions involving smaller subregions. One of these differences involve a small segment of H19ql3.4 genes whose murine counterparts have been transposed out of the large Mmu7/H19q conserved synteny region into a separate linkage group located on mouse chromosome 17. The five internal rearrangements are clustered together at two sites, suggesting either the coincidence of rearrangement events or their common association with unstable DNA sequences. Interestingly, both rearranged regions are occupied by large tandemly clustered gene families, suggesting that these locally repeated sequences may have contributed to their evolutionary instability. More recently, we have extended mapping studies to include other regions, and are working to define the borders of mouse-human syntenic segments on a broader, genome-wide scale.
As another aspect of this collaborative project, we have explored means of exploiting mouse-human genomic conservation in the isolation of functionally-significant sequences from large cloned regions of human DNA. Using a model system comprised of sequenced mouse and human cosmids spanning the XRCC1 gene, we have succeeded in developing a method for isolating exons as well as conserved regulatory sequences with high efficiency. We have recently applied this methodology to the analysis of two larger genomic regions (~300 kb each) spanned by overlapping human cosmids and parallel sets of mouse P1 clones. Our analysis of clones isolated from these two regions, which include several known genes as well as large segments of unexplored DNA, will be presented. Because of its relative simplicity and ability to purify both coding and regulatory regions at high yield, this conserved-element purification method holds great promise as an efficient tool for gene discovery in cloned genomic regions.
[1] Human Genome Center, P.O. Box 808, Lawrence Livermore National Laboratory, Livermore, CA 94550.
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.