Small open reading frames associated with morphogenesis are hidden in plant genomes

被引：140

作者：

Hanada, Kousuke ^{[1
,2
,3
]}

Higuchi-Takeuchi, Mieko ^{[1
]}

Okamoto, Masanori ^{[1
,4
]}

Yoshizumi, Takeshi ^{[1
]}

Shimizu, Minami ^{[1
]}

Nakaminami, Kentaro ^{[1
]}

Nishi, Ranko ^{[1
]}

Ohashi, Chihiro ^{[1
]}

Iida, Kei ^{[2
]}

Tanaka, Maho ^{[1
]}

Horii, Yoko ^{[1
]}

Kawashima, Mika ^{[1
]}

Matsui, Keiko ^{[1
]}

Toyoda, Tetsuro ^{[1
,2
]}

Shinozaki, Kazuo ^{[1
]}

Seki, Motoaki ^{[1
]}

Matsui, Minami ^{[1
]}

机构：

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

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

[3] Kyushu Inst Technol, Dept Biosci & Bioinformat, Frontier Res Acad Young Researchers, Iizuka, Fukuoka 8208502, Japan

[4] Univ Calif Riverside, Dept Bot & Plant Sci, Ctr Plant Cell Biol, Riverside, CA 92521 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2013年 / 110卷 / 06期

基金：

日本学术振兴会; 日本科学技术振兴机构;

关键词：

transcriptome; phenome; Agilent custom microarray; transgenic plant; peptide hormone; ARABIDOPSIS-THALIANA; SECRETORY PEPTIDE; GENE-EXPRESSION; RNA-SEQ; POLYPEPTIDE; DIFFERENTIATION; OVEREXPRESSION; PROLIFERATION; TRANSCRIPTS; PREDICTION;

D O I：

10.1073/pnas.1213958110

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

It is likely that many small ORFs (sORFs; 30-100 amino acids) are missed when genomes are annotated. To overcome this limitation, we identified similar to 8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis thaliana genome. However, the question remains as to whether these coding sORFs play functional roles. Using a designed array, we generated an expression atlas for 16 organs and 17 environmental conditions among 7,901 identified coding sORFs. A total of 2,099 coding sORFs were highly expressed under at least one experimental condition, and 571 were significantly conserved in other land plants. A total of 473 coding sORFs were overexpressed; similar to 10% (49/473) induced visible pheno-typic effects, a proportion that is approximately seven times higher than that of randomly chosen known genes. These results indicate that many coding sORFs hidden in plant genomes are associated with morphogenesis. We believe that the expression atlas will contribute to further study of the roles of sORFs in plants.

引用

页码：2395 / 2400

页数：6

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