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Keywords:

  • enhancer detection;
  • phylogenetic footprinting;
  • synteny;
  • gene desert;
  • mouse;
  • human genome;
  • highly conserved noncoding regions;
  • hox cluster

Abstract

All vertebrates share a similar early embryonic body plan and use the same regulatory genes for their development. The availability of numerous sequenced vertebrate genomes and significant advances in bioinformatics have resulted in the finding that the genomic regions of many of these developmental regulatory genes also contain highly conserved noncoding sequence. In silico discovery of conserved noncoding regions and of transcription factor binding sites as well as the development of methods for high throughput transgenesis in Xenopus and zebrafish are dramatically increasing the speed with which regulatory elements can be discovered, characterized, and tested in the context of whole live embryos. We review here some of the recent technological developments that will likely lead to a surge in research on how vertebrate genomes encode regulation of transcriptional activity, how regulatory sequences constrain genomic architecture, and ultimately how vertebrate form has evolved. Developmental Dynamics 235:870–885, 2006. © 2006 Wiley-Liss, Inc.