ABI Sustaining: The REDfly database of transcriptional regulatory elements

Suny At Buffalo, Amherst NY

Investigators

Abstract

Transcriptional cis - regulatory modules (CRMs) are DNA sequences 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 for many areas of biology, these sequences are not well-documented. The REDfly (Regulatory Element Database for Fly) database 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. It's records include over 16,000 experimentally verified CRMs and 2000 TFBSs along with their DNA sequence, their associated genes, and the gene 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 and maintenance of the database so that it remains up to date and functions with maximum utility for its users. 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 current project also has a valuable undergraduate education component. It will continue to be the focus of a University at Buffalo course "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. In a new effort, a REDfly unit will be introduced into a Developmental Biology course at Baruch College-CUNY, one of the nation's most diverse campuses. Students who excel in the class will be invited to Buffalo to participate in the Summer Undergraduate Research Experience (SURE) program and serve as REDfly curators. The specific objectives of this Sustaining Award are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being discovered and reported in the literature, and to maintain the REDfly site in a manner that will maximize its utility to the research community. The focus is on: (1) Curation. REDfly will be kept up - to - date as new studies are published. Emphasis will remain on in vivo assays, but in vitro studies will be included where encountered and appropriate. (2) Education. The PI will continue to use REDfly as the basis for his "Genome Annotation" course. A REDfly unit will be introduced in an undergraduate course at Baruch College-CUNY, and bring up to two course alumni to Buffalo each summer to work on REDfly curation as a part of the University at Buffalo Medical School's Summer Research Experiences for Undergraduates (SURE) program. (3) Service. REDfly will continue to serve its user community with a high degree of responsiveness, including rapid response to queries, custom searches and downloads on request, error correction, and support for undergraduate courses. (4) General maintenance. REDfly will be maintained in peak operating condition through identification and correction of programming bugs, regular updates to genome annotations imported from FlyBase and other sources, active maintenance of links to outside resources, software and/or hardware updates, etc. These activities will ensure that REDfly data continue to be available as an important resource for the scientific community. The REDfly database can be found at http://redfly.ccr.buffalo.edu. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.