Decoding noncoding regulatory DNAs in metazoan genomes

Summary form only given. The recent revelation that the human genome contains only ∼30,000 genes underscores the importance of gene regulation in generating organismal diversity. Cis-regulatory DNAs, or enhancers, are short stretches of DNA-300 bp to 1,000 bp in length-that control gene expression. This DNA accounts for a substantial fraction of metazoan genomes, but is largely invisible. It cannot be identified by simple sequence inspection. One of the outstanding issues in the post-genome era is whether there is a "cis-regulatory code" that links primary DNA sequence with gene expression patterns. We have used a combination of bioinformatics methods and functional assays to determine whether coordinately regulated genes share a common "grammar".