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The Maize TF ome – development of a transcription factor open reading frame collection for functional genomics
Author(s) -
Burdo Brett,
Gray John,
GoettingMinesky Mary P.,
Wittler Bettina,
Hunt Matthew,
Li Tai,
Velliquette David,
Thomas Julie,
Gentzel Irene,
Brito Michael dos Santos,
MejíaGuerra Maria Katherine,
Connolly Layne N.,
Qaisi Dalya,
Li Wei,
Casas Maria I.,
Doseff Andrea I.,
Grotewold Erich
Publication year - 2014
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12623
Subject(s) - orfs , open reading frame , genome , biology , computational biology , gene , genetics , functional genomics , genomics , peptide sequence
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/).