Gene regulatory information is encoded in the promoter regions formed by cis -regulatory elements that bind specific transcription factors (TFs). Hence, establishing the architecture of plant promoters is fundamental to understanding gene expression. AGRIS ( http://arabidopsis.med.ohio-state.edu) is an information resource of Arabidopsis promoter sequences, TFs, and their target genes.
AGRIS currently contains two databases, AtTFDB ( A. thaliana TF database) and At cis DB ( A. thaliana cis -regulatory element database). AtTFDB contains approximately 1,800 transcription factors identified directly through BLAST and motif searches and arranged into ~50 primary families. At cis DB consists of the 5’ regulatory sequences of ~28,000 annotated genes with a description of putative cis -regulatory elements. A user can search the At cis DB and for each result, the user can view the promoter sequence in both directions, with a color-coded graphical display of the type of binding site predicted. AtRegNet (http://arabidopsis.med.ohio-state.edu/RGNet/) provides a powerful tool to visualize experimentally-verified Arabidopsis regulatory motifs.
AGRIS provides one of the first attempts to provide the necessary software tools to incorporate Arabidopsis TFs and their putative binding sites on all genes, thereby initiating the identification of transcriptional regulatory networks.
In addition to the computational analysis of TF-DNA interactions, we are utilizing a combination of TF-GR (glucocorticoid receptor) coupled with expression arrays and chromatin immunoprecipitation (ChIP) and ChIP-chip to establish regulatory motifs in Arabidopsis and maize. The protocols currently being used are available at http://skull.med.ohio-state.edu/arabidopsis/protocols.html.