Solving a Bottleneck in Functional Genomics: Rules for Efficient Computational Identification of Cis-Regulatory Elements by Interspecific Sequence Comparison

California Institute Of Technology, Pasadena CA

Investigators

Abstract

0212869 Cameron Understanding the details of how individual cis-regulatory elements function and how the gene regulatory networks they form control developmental process is crucial to understanding how the genome works, how development works, and how evolution works. An effective method of locating individual cis-regulatory elements is comparative sequence analysis conducted at appropriate divergence times to reveal conserved elements. Current results show that this approach may yield a more than 10-fold increase in rate of experimental cis-regulatory element discovery, compared to the most efficient "blind" search methods. However, general rules for carrying out such analyses are not yet known, and initial work has shown very different degrees of similarity between genomic regions surrounding different genes in a single pair of sea urchin species. These investigators propose to determine the rules for efficient cis-regulatory sequence prediction by interspecific sequence analysis. To this end they will analyze and then test by gene transfer putative cis-regulatory elements identified in the vicinity of about 20 different genes, using several different echinoderm species that display a range of phylogenetic relatedness. The sea urchin embryo is a model system of choice in which this method can be quickly and effectively explored: species separated by various known evolutionary distances are available; they have already established methods for comparative prediction of conserved cis-regulatory sequence for one sea urchin species pair and shown that the methods work; and there is a practical high throughput gene transfer technology available. These investigators will construct BAC libraries for 6-8 species including sea urchins, and for more distant comparisons, a sea star and a hemichordate. Sequence of BACs containing the set of genes to be studied will be obtained, and they will then identify putative cis-regulatory regions for the candidate genes selected, as indicated by interspecific sequence comparison at diverse distances. These DNA fragments will be tested for cis-regulatory capability by gene transfer. Not only will this approach reveal rules for computational cis-regulatory analysis, but it will also support the extension of the current repertoire of BAC libraries, improve computational tools, and generate more efficient laboratory methods for this essential research area.