ABI Sustaining: The REDfly database of transcriptional regulatory elements

Suny At Buffalo, Amherst NY

Investigators

Abstract

The State University of New York at Buffalo is awarded a sustaining grant to support ongoing operation of The REDfly (Regulatory Element Database for Fly). REDfly is a freely available and easily web-accessible resource of significant value to the biological community, both for wet-lab biologists and for bio-informaticians. Undergraduate students will play a significant role in this project as the primary curators for ongoing regulatory element annotation. In addition, REDfly has a demonstrated utility for education and training. REDfly has been the source of data for student projects in bioinformatics/computational biology at several schools. It is also the focus of a seminar course for undergraduates taught by the PI, "Genome Annotation," in which the students participate in annotating regulatory elements for entry into REDfly, thus making genuine contributions to the research community while learning the techniques of genome annotation and biocuration and the science of gene regulation. The students learn how to use an array of web-based sequence analysis tools, gain an appreciation for the complexities of gene expression and anatomy, develop skills in reading the primary literature, and are exposed to a diversity of experimental systems and approaches. Transcriptional cis-regulatory modules (CRMs) are a major class of genomic sequence elements required for regulating gene expression - determining when and where genes are turned "on" and "off." CRMs play critical roles with respect to normal variation between individuals, birth defects, chronic diseases, and evolution. Despite the clear importance of CRMs for many areas of biology, these sequences are vastly underrepresented in current genome annotations. REDfly helps fill this gap in CRM annotation by curating known CRMs and transcription factor binding sites (TFBS) for the important research organism Drosophila melanogaster (fruit fly). REDfly is the most detailed existing platform for regulatory element annotation for any animal. Its records include over 1850 experimentally verified CRMs and 2000 TFBSs along with their DNA sequence, their associated genes, and the expression patterns they direct. REDfly is a well-used and valuable resource for the genomics, bioinformatics, and Drosophila communities and is an important platform for supporting hypothesis-driven empirical and computational research. It has contributed to numerous studies in multiple areas relating to non-Drosophila as well as Drosophila systems including CRM biology, CRM discovery, construction of regulatory network models, interpretation of genomic datasets, and CRM evolution. The current project will focus on continued curation of the database and is anticipated to increase the number of records by five-fold or more. This will ensure that REDfly continues to be available as an important source of raw data for analysis, hypothesis generation, assessment and validation, and empirical research in molecular and developmental biology, genetics, genomics, bioinformatics, and evolution. The REDfly Database can be found at http://redfly.ccr.buffalo.edu.