title: An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family.
abstract: AP2/EREBP transcription factors (TFs) play functionally important roles in plant growth and development, especially in hormonal regulation and in response to environmental stress. Here we reported verification and correction of annotation through an exhaustive cDNA cloning and sequence analysis performed on 145 of 147 gene family members. A RACE analysis performed on genes with potential in-frame up-stream ATG codon resulted in identification of At2g28520 as an authentic AP2/EREBP member and corrected ORF annotations for three other members. A further phylogenetic analysis of this updated and likely complete family divided it into three major subfamilies. The expression patterns of the AP2/EREBP family members among the 11 organ or tissue types were examined using an oligo microarray and their hormonal and environmental responsiveness were further characterized using cDNA custom macroarrays. These detailed expression profile results provide strong support for a role for AP2/EREBP family members in development and in response to environmental stimuli, and a foundation for future functional analysis of this gene family.
authors.affiliation: The National Laboratory of Protein Engineering and Plant Genetic Engineering Peking University, 100871, Beijing, China.
authors.forename: Jian-Xun
authors.initials: JX
authors.lastname: Feng
authors.forename: Di
authors.initials: D
authors.lastname: Liu
authors.forename: Yi
authors.initials: Y
authors.lastname: Pan
authors.forename: Wei
authors.initials: W
authors.lastname: Gong
authors.forename: Li-Geng
authors.initials: LG
authors.lastname: Ma
authors.forename: Jing-Chu
authors.initials: JC
authors.lastname: Luo
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
authors.forename: Yu-Xian
authors.initials: YX
authors.lastname: Zhu
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry; D003001:Cloning, Molecular; D003062:Codon; D019295:Computational Biology; D018076:DNA, Complementary / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D004777:Environment; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D018398:Homeodomain Proteins / Q000737:chemistry; D006728:Hormones / Q000378:metabolism; D008390:Markov Chains; D008957:Models, Genetic; D009687:Nuclear Proteins / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry; D017434:Protein Structure, Tertiary; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D014466:Ultraviolet Rays
chemical_list: C499534:APETALA2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D003062:Codon; D018076:DNA, Complementary; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D006728:Hormones; D009687:Nuclear Proteins; D010940:Plant Proteins; D014157:Transcription Factors; C093680:ethylene-responsive element binding protein