title: Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice.
abstract: Ionizing radiation (IR) affects gene expression from plant genomes. To monitor the genome-wide transcriptional changes induced by three types of IR, we used the rice Affymetrix GeneChip microarray to identify genes that are up- or down-regulated by gamma rays (GAs), cosmic rays (CRs) and ion beams (IBs). The overall expression patterns in rice seedlings generated from seeds exposed to GAs and IBs were similar but differed for CRs exposure. Expression profiles of genes involved in metabolic pathways and cellular response were identified using MapMan analysis. This result revealed that IRs induced gene expression related to sucrose-starch metabolisms; sugar and starch accumulation was significantly increased in response to three types of IR in rice. In addition, we compared the genes commonly up- or down-regulated by exposure to three types of IR and identified 53 candidate radio marker genes (RMGs) that were differentially regulated by radiation exposure but not by other stresses. Among these genes, we selected six RMGs commonly applicable to different types of IR by specific coexpression networks using the algorithm for the reconstruction of accurate cellular networks (aracne) and confirmed the expression of these genes by reverse transcription-polymerase chain reaction (RT-PCR) analysis. Our results provided insight into the mechanisms of the responses to different types of IR and identified multiple marker genes to predict sensitivity to three types of IR.
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, Republic of Korea.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Hwang
authors.forename: Sun-Goo
authors.initials: SG
authors.lastname: Hwang
authors.forename: Sun-Hee
authors.initials: SH
authors.lastname: Kim
authors.forename: Kyung Jun
authors.initials: KJ
authors.lastname: Lee
authors.forename: Cheol Seong
authors.initials: CS
authors.lastname: Jang
authors.forename: Jin-Baek
authors.initials: JB
authors.lastname: Kim
authors.forename: Sang Hoon
authors.initials: SH
authors.lastname: Kim
authors.forename: Bo-Keun
authors.initials: BK
authors.lastname: Ha
authors.forename: Joon-Woo
authors.initials: JW
authors.lastname: Ahn
authors.forename: Si-Yong
authors.initials: SY
authors.lastname: Kang
authors.forename: Dong Sub
authors.initials: DS
authors.lastname: Kim
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects*; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011839:Radiation, Ionizing; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D010940:Plant Proteins