Eukaryotic cells package nuclear DNA in a variety of highly ordered structures, collectively termed "chromatin". The primary function of chromatin is to maintain a restrictive ground state wherein the DNA is inaccessible to the transcriptional machinery but is accessible to specific transcriptional activators and repressors that recruit multi-protein complexes capable of remodeling chromatin locally to allow transcription to occur. ChromDB (Plant Chromatin Database) was established originally as a project-specific database to display the results of a previous Plant Genome Research Program grant that examined the functional genomics of chromatin proteins in Arabidopsis and maize. The Arabidopsis genomic sequence and, once available, the maize EST collection were queried using protein domains from known yeast, fly, human, and nematode chromatin genes to assemble a collection of putative plant chromatin proteins. Chromatin proteins from rice and the single-celled alga Chlamydomonas reinhardtii were added to the database to provide more phylogenetic perspective to the database. This award supports the broad expansion of ChromDB from a project-oriented database to a community database supporting the entire plant biology community.
The complement of chromatin proteins will be increased to include all plant species for which either genomic or cDNA sequences are available in order to provide a comprehensive, comparative summary of predicted protein domains, transcript splicing products, molecular phylogenetic relationships and molecular signatures of selection. ChromDB will integrate and display all available community data regarding gene function such as mutant phenotypes, biochemical activities and properties, transcript and protein expression patterns, physical and genetic interactions between genes and proteins, and localization of chromatin proteins within the nucleus. ChromDB will provide a public annotation forum for researchers to submit and present this information with the submissions reviewed by an editorial advisory board.
An educational outreach program will provide experience for high school teachers in the area of bioinformatics and functional genomics. There are three objectives associated with this outreach: (1) to produce, in partnership with teachers, a set of web-based, integrated teaching modules to introduce students to the biological importance of chromatin by way of discussions centered on DNA, genes, and chromosomes, as well introduce students to the scientific method and experimental analysis; (2) to provide teachers with working experience in select aspects of bioinformatics; and (3) to develop a protocol for experiments to be conducted in classroom locations under circumstances of limited supplies and equipment.
All project-generated results and materials will be available at the database site, www.chromdb.org/.