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SIFTING SEQUENCE FOR FUNCTION: EXPLOITING THE MOUSE.   Eddy Rubin, Lawrence Berkeley National Laboratory, University of California, Berkeley, California

     One of the major challenges in the post genomic era will be the identification of sequences participating in the regulatory circuitry controlling gene expression.  For the analysis of genomic DNA, algorithms and databases are available facilitating the identification of those sequences encoding genes.  While these sorts of computational aids are largely not available for the identification of noncoding sequences participating in gene regulation, cross-species sequence comparisons provide a robust means for identifying putative gene regulatory sequences.  Using this approach to identify gene regulatory sequences we have examined orthologous regions of human 5q31 and mouse chromosome 11, DNA of biomedical importance due to the clustering of a several interleukin genes.  The functional properties of the largest noncoding element (401 BP >85% conserved between humans and mice) located in the IL4, IL13 intergenic interval were examined in depth.  To identify its function, knockout mice lacking this 401 BP element as well as YAC transgenics with and without the element were examined.  Analysis of the animals revealed that this noncoding sequence plays a prominent role in the regulation of IL4, IL13 and IL5 genes that are spread over 120KB.  The comparative genomic strategy used here for identifying noncoding sequence of biological import has led to the discovery of a regulatory element that acts over significant genomic distance to coordinate the expression of several genes involved in the inflammatory response.  We have carried out similar studies in other regions of the genome that further illustrate the power of cross-species sequence analysis coupled with functional studies in mice to investigate the gene regulatory circuitry of mammals.