Abstract
Phylogenetic footprinting has revealed that cis-regulatory modules consist of clusters of conserved DNA sequences. We have generated a Drosophila melanogaster genomic database of conserved sequence clusters (CSCs) to facilitate enhancer discovery and analysis of their sub-structure. The database consists of >100,000 CSCs gleaned from EvoPrints spanning over 90% of the genome. To identify related enhancers based on shared conserved sequence elements, we have developed database search and alignment algorithms, collectively known as cis-Decoder. These web-accessible tools initially identify conserved repeat elements within an EvoPrinted input enhancer and then search the database for CSCs that score highly against the input enhancer. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. The genome-wide CSC database and cis-Decoder algorithms can be used to discover and analyze cis-regulatory DNA involved in any developmental process. Developmental Dynamics, 2011. © 2011 Wiley-Liss, Inc.
No comments:
Post a Comment