Steven G Kuntz et al. (2005) International Worm Meeting "Comparative sequence analysis using novel nematode sequences for efficient cis-regulatory element identification in a Hox cluster."

Erich M Schwarz, Steven G Kuntz, John DeModena, Paul W Sternberg, Tristan DeBuysscher, Barbara J Wold

[International Worm Meeting, 2005]

Understanding the transcriptional regulation of developmentally important genes can be aided by cross-species genetic comparisons. We hope to learn how to most efficiently infer regulatory regions from comparative sequence analysis. Such comparative analysis was used to dissect a large regulatory region in C. elegans, the non-coding sequence surrounding the Hox cluster genes lin-39 and ceh-13. The region studied includes 19 kb of intergenic sequence as well as 8 kb of intronic sequence; exons were not included. The corresponding region in Caenorhabditis spp. CB5161 and PS1010 was sequenced; comparison to C. elegans and C. briggsae showed that only 2% of it was strongly conserved. Twelve clusters of conserved elements -- each element being 18 to 40 bp long -- could be identified. Near ceh-13, the conserved elements are entirely upstream. However, near lin-39 the sites are evenly distributed upstream and in introns. For in vivo testing of these putative regulatory elements, flanking sequences were included upstream and downstream of each element. One element has been previously identified as an enhancer element, functional during embryogenesis (Streit et al. [2002], Dev. Biol. 242, 96-108). A second computationally identified element corresponds to the microRNA mir-231. As of March 2005, a third element was demonstrated to drive strong reporter expression in the posterior bodywall muscle when used with a basal promoter. Further analysis will be used to determine the regulatory properties of each element, as well as combined effects of these elements.