The REDfly Database of Transcriptional Regulatory Elements
Halfon, Marc Principal Investigator
MetadataShow full item record
This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). The State University of New York at Buffalo has received a grant to create a database and software tools to facilitate the study of gene regulation, through transcriptional cis-regulatory modules (CRMs). CRMs are a major class of genomic sequence elements required for the temporal and spatial control of gene expression. CRMs play critical roles with respect to normal phenotypic variation, birth defects, chronic diseases, and evolution. Despite this clear importance of CRMs for many areas of biology, our knowledge of these sequences is surprisingly limited. CRMs are vastly underrepresented in current genome annotations, in part because most CRMs are uncharacterized, but also because there has been little effort to curate the literature for known CRMs or to develop appropriate databases to house CRM information. This project, by producing a well-annotated collection of known CRMs, will be of significant use in a number of important areas, including studies of transcriptional regulation, of the evolution of CRMs and new gene functions, and of genome structure. The project also provides training data for computational approaches to CRM discovery, leading to improved methods for identifying uncharacterized CRMs. The project has constructed the first database of known CRMs for any animal, the REDfly (Regulatory Element Database for Fly) database of regulatory elements for the fruit fly Drosophila melanogaster. Funding under this award is allowing for the continued development and expansion of REDfly into a fully comprehensive resource for Drosophila and for its extension to regulatory elements from vertebrate model organisms, including the zebrafish and mouse. Analysis of the REDfly data will lead to the discovery of new important features of CRMs and to the generation of exciting new hypotheses about gene regulation that are being tested experimentally in the laboratory. REDfly also serves as a useful resource for education and training in genomics, gene regulation, and genome annotation at the graduate, undergraduate, and secondary school levels through a variety of courses, workshops, and informal training activities. These activities create in REDfly a comprehensive repository for cis-regulatory sequence and expression pattern data for three major metazoan model organisms, making REDfly the most powerful available resource for large-scale studies of the composition, organization, and evolution of transcriptional cis-regulatory elements. The REDfly database can be found at http://redfly.ccr.buffalo.edu.