Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information

The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.

The Maize TFome--development of a transcription factor open reading frame collection for functional genomics

Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/).