GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses    

Abstract

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

“…GO enrichment analysis identified genes differentially regulated in both species as enriched in transcription factor-related GO terms, such as GO:0006355 "regulation of transcription, DNA-templated." This enrichment was further confirmed in a separate test for enrichment of genes annotated as transcription factors in the GRASSIUS database (Yilmaz et al, 2009). No nontranscription factor-related GO term showed significant enrichment when compared with the population of gene pairs that were syntenically conserved between both species.…”

“…Transcription factor enrichment was calculated using the maize transcription factor list from GRASSIUS (Yilmaz et al, 2009). …”

RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

“…The recently annotated MEG family members (Xiong et al, 2014) were also incorporated. Annotation of TF family members were based on information from Plant Transcription Factor Database v3.0 (Jin et al, 2014) and GrassTFDB of GRASSIUS Yilmaz et al, 2009). Annotation of zein genes in the B73 genome was based on the information as summarized by Chen et al (2014).…”

The OsMYB30 Transcription Factor Suppresses Cold Tolerance by Interacting with a JAZ Protein and Suppressing β-Amylase Expression

“…In view of the potential roles of the R2R3 MYB genes in cold stress regulation, we chose one cold-responsive MYB gene (LOC_Os02g41510) from the rice microarray database (GSE71680) and named it OsMYB30 according to GRASSIUS (http://grassius.org/grasstfdb.html; Yilmaz et al, 2009). We applied quantitative realtime PCR (qPCR) to inspect the expression profile of OsMYB30 under multiple hormone treatments and abiotic stresses at the rice seedling stage.…”