GRASSIUS provides a public knowledgebase composed by a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a "one-stop" resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.
GRASSIUS currently contains regulatory information on maize, rice, sorghum, sugarcane, Setaria and Brachypodium. However, as genome sequencing and annotation efforts in other grasses continue to progress, GRASSIUS will expand to include information on them as well. The success of this endeavor is largely dependent on community contributions, thus we hope to hear from you soon.
GRASSIUS integrates information from several large databases. GrassTFDB contains information on TFs, their DNA-binding properties and the genes that they have been shown to bind/regulate. TFs are divided into ~60 families based on unique structural characteristics. Information on TFs can be accessed individually by plant (i.e., accessing MaizeTFDB, RiceTFDB, SorghumTFDB or CaneTFDB), or by TF family (e.g., by searching GrassTFDB for a particular TF family, for example MYB). GrassTFDB also contains information on the availability of clones for particular TFs, as part of publicly available TFome collections containing constantly increasing numbers of TFs in recombination-ready vectors. GrassPROMDB will contain information on gene regulatory sequences from the various grasses, and when available, information on which regulatory sequences are important for gene expression. Integrating the information contained in GrassTFDB and GrassPROMDB will be GrassREGNET, a database that will allow the visualization of regulatory motifs and networks across the grasses.
Gene models for TFs are constantly updated with improvements in genome annotations. Currently, GRASSIUS harbors data obtained from the following genome annotations: