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

Abstract

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/).

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites

“…Plasmids (15 mg) were transformed into protoplasts isolated from F1 seedlings of B73xMo17, as described (Burdo et al, 2014). Protoplasts were incubated for 18 to 22 h in the dark at 25°C prior to monitoring GFP expression using confocal microscopy (Leica DMIRE2; excitation, 488 nm; emission 500 to 530 nm) and chlorophyll autofluorescence (excitation, 543 nm; emission 580 to 650 nm).…”

Auxin signaling modules regulate maize inflorescence architecture

“…The underlying molecular cause of the Bif1 mutant has remained unknown since its discovery in 1977 (24). On the basis of its auxin-related phenotype and semidominance, we reasoned that BIF1 might encode one of the 38 maize Aux/IAA genes (27,28), known negative regulators of auxin signaling that give rise to dominant mutants (7). We searched the maize genome for Aux/IAAs that were located in the region of chromosome 8, where the BIF1 locus was previously mapped (25).…”

Multivariate analyses of root phenotype and dynamic transcriptome underscore valuable root traits and water‐deficit responsive gene networks in maize

“…The maize TF open reading frame collection identified 2017 unique maize TFs. Earlier studies have showed that a wide range of these TF families hold relevance with drought stress response (Burdo et al., ). In this study, an over‐representation of GO term related to transcription regulatory activity was detected with the long‐term PEG treatment (72 hr), which identified 66 up‐regulated TFs in the drought tolerant line (Figure d).…”

“…The resulting significantly over-and under-represented GO categories were graphically interpreted by ggplot2 package (Wickham, 2009). Annotation of transcriptional factor family members was based on information from GrassTFDB of GRASSIUS (Burdo et al, 2014).…”