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

Author(s):Show less -

Burdo, Brett ^[1] ; Gray, John ^[2] ; Goetting-Minesky, Mary P. ^[2] ; Wittler, Bettina ^[1] ; Hunt, Matthew ^[1] ; Li, Tai ^[2] ; Velliquette, David ^[2] ; Thomas, Julie ^[2] ; Gentzel, Irene ^[1] ; Brito, Michael dos Santos ^{[3, 1]} ; Mejia-Guerra, Maria Katherine ^{[1, 4]} ; Connolly, Layne N. ^[1] ; Qaisi, Dalya ^[1] ; Li, Wei ^{[5, 6]} ; Casas, Maria I. ^{[1, 4]} ; Doseff, Andrea I. ^{[3, 7]} ; Grotewold, Erich ^{[1, 7]}

Affiliation

^[1] Ohio State Univ, Ctr Appl Plant Sci CAPS, Columbus, OH 43210 - USA

^[2] Univ Toledo, Dept Biol, Toledo, OH 43606 - USA

^[3] Univ Estadual Campinas, Inst Biol, Dept Plant Biol, BR-13083970 Campinas, SP - Brazil

^[4] Ohio State Univ, Mol Cellular & Dev Biol Grad Program, Columbus, OH 43210 - USA

^[5] Ohio State Univ, Dept Internal Med, Columbus, OH 43210 - USA

^[6] Ohio State Univ, Heart & Lung Res Inst, Columbus, OH 43210 - USA

^[7] Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 - USA

• Document type: Journal article
• Source: Plant Journal; v. 80, n. 2, p. 356-366, OCT 2014.
• Web of Science Citations: 21

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/). (AU)

• FAPESP's process: 12/20486-2 - Identification of target genes regulated by transcription factor SSH1 in sugarcane, using ChIP-Seq assay
• Grantee: Michael dos Santos Brito
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor