RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions

BMC Plant Biology

Research Article

Hirokazu Handa¹  Takashi Matsumoto¹  Youko Oono¹  Takayuki Yazawa²  Yuhya Wakasa³  Shimpei Hayashi³  Kenjirou Ozawa³  Fumio Takaiwa³ 

[1] Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan;Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, 305-8602, Tsukuba, Ibaraki, Japan;Government and Public Corporation Information Systems, Hitachi Co., Ltd, 2-4-18 Toyo, 135-8633, Koto-ku, Tokyo, Japan;Functional Transgenic Crops Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, 305-8602, Tsukuba, Ibaraki, Japan;

关键词: Gene targeting;    ER stress response;    Microarray;    Oryza sativa;    RNA sequencing;    Transcriptome;   

DOI  :  10.1186/1471-2229-14-101

 received in 2013-08-21, accepted in 2014-04-11,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe endoplasmic reticulum (ER) stress response is widely known to function in eukaryotes to maintain the homeostasis of the ER when unfolded or misfolded proteins are overloaded in the ER. To understand the molecular mechanisms of the ER stress response in rice (Oryza sativa L.), we previously analyzed the expression profile of stably transformed rice in which an ER stress sensor/transducer OsIRE1 was knocked-down, using the combination of preliminary microarray and quantitative RT-PCR. In this study, to obtain more detailed expression profiles of genes involved in the initial stages of the ER stress response in rice, we performed RNA sequencing of wild-type and transgenic rice plants produced by homologous recombination in which endogenous genomic OsIRE1 was replaced by missense alleles defective in ribonuclease activity.ResultsAt least 38,076 transcripts were investigated by RNA sequencing, 380 of which responded to ER stress at a statistically significant level (195 were upregulated and 185 were downregulated). Furthermore, we successfully identified 17 genes from the set of 380 ER stress-responsive genes that were not included in the probe set of the currently available microarray chip in rice. Notably, three of these 17 genes were non-annotated genes, even in the latest version of the Rice Annotation Project Data Base (RAP-DB, version IRGSP-1.0).ConclusionsTherefore, RNA sequencing-mediated expression profiling provided valuable information about the ER stress response in rice plants and led to the discovery of new genes related to ER stress.

【 授权许可】

Unknown   
© Wakasa et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.