title: Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays.
abstract: The phytohormone abscisic acid (ABA) plays important roles in the induction and maintenance of seed dormancy. Although application of exogenous ABA inhibits germination, the effects of exogenous ABA on ABA-mediated gene transcription differ from those of endogenous ABA. To understand how endogenous ABA regulates the transcriptomes in seeds, we performed comprehensive expression analyses using whole-genome Affymetrix tiling arrays in two ABA metabolism mutants - an ABA-deficient mutant (aba2) and an ABA over-accumulation mutant (cyp707a1a2a3 triple mutant). Hierarchical clustering and principal components analyses showed that differences in endogenous ABA levels do not influence global expression of stored mRNA in dry seeds. However, the transcriptome after seed imbibition was related to endogenous ABA levels in both types of mutant. Endogenous ABA-regulated genes expressed in imbibed seeds included those encoding key ABA signaling factors and gibberellin-related components. In addition, cohorts of ABA-upregulated genes partially resembled those of dormant genes, whereas ABA-downregulated genes were partially overlapped with after-ripening-regulated genes. Bioinformatic analyses revealed that 6105 novel genes [non-Arabidopsis Genome Initiative (AGI) transcriptional units (TUs)] were expressed from unannotated regions. Interestingly, approximately 97% of non-AGI TUs possibly encoded hypothetical non-protein-coding RNAs, including a large number of antisense RNAs. In dry and imbibed seeds, global expression profiles of non-AGI TUs were similar to those of AGI genes. For both non-AGI TUs and AGI code genes, we identified those that were regulated differently in embryo and endosperm tissues. Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought.
authors.affiliation: RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Okamoto
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Tatematsu
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsui
authors.forename: Taeko
authors.initials: T
authors.lastname: Morosawa
authors.forename: Junko
authors.initials: J
authors.lastname: Ishida
authors.forename: Maho
authors.initials: M
authors.lastname: Tanaka
authors.forename: Takaho A
authors.initials: TA
authors.lastname: Endo
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kamiya
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Eiji
authors.initials: E
authors.lastname: Nambara
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D018525:Germination; D009154:Mutation; D010937:Plant Growth Regulators / Q000378:metabolism; D025341:Principal Component Analysis; D018749:RNA, Plant / Q000235:genetics; D012639:Seeds / Q000235:genetics / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D010937:Plant Growth Regulators; D018749:RNA, Plant; D000040:Abscisic Acid