Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays

被引：117

作者：

Okamoto, Masanori ^{[1
]}

Tatematsu, Kiyoshi ^{[3
]}

Matsui, Akihiro ^{[1
]}

Morosawa, Taeko ^{[1
]}

Ishida, Junko ^{[1
]}

Tanaka, Maho ^{[1
]}

Endo, Takaho A. ^{[2
]}

Mochizuki, Yoshiki ^{[2
]}

Toyoda, Tetsuro ^{[2
]}

Kamiya, Yuji ^{[1
]}

Shinozaki, Kazuo ^{[1
]}

Nambara, Eiji ^{[4
]}

Seki, Motoaki ^{[1
,5
]}

机构：

[1] RIKEN Plant Sci Ctr, Kanagawa 2300045, Japan

[2] RIKEN Bioinformat & Syst Engn Div, Kanagawa 2300045, Japan

[3] Natl Inst Basic Biol, Okazaki, Aichi 4448585, Japan

[4] Univ Toronto, Dept Cell & Syst Biol, Toronto, ON M5S 3B2, Canada

[5] Yokohama City Univ, Kihara Inst Biol Res, Kanagawa 2440813, Japan

来源：

PLANT JOURNAL | 2010年 / 62卷 / 01期

关键词：

abscisic acid; Arabidopsis; seed dormancy; germination; tiling array; non-protein-coding RNA; PENTATRICOPEPTIDE REPEAT PROTEINS; GENE-EXPRESSION; MESSENGER-RNA; TOMATO SEEDS; MICROPYLAR ENDOSPERM; RESERVE MOBILIZATION; GERMINATION; DORMANCY; THALIANA; BIOSYNTHESIS;

D O I：

10.1111/j.1365-313X.2010.04135.x

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

P>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-Aradopsis 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.

引用

页码：39 / 51

页数：13

共 72 条

[51] Diamonds in the rough:: mRNA-like non-coding RNAs [J].