title: Linear Energy Transfer-Dependent Change in Rice Gene Expression Profile after Heavy-Ion Beam Irradiation.
abstract: A heavy-ion beam has been recognized as an effective mutagen for plant breeding and applied to the many kinds of crops including rice. In contrast with X-ray or γ-ray, the heavy-ion beam is characterized by a high linear energy transfer (LET). LET is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET-dependent regulated genes, whose expression level increased with the rise of LET value, were also identified. Gene ontology (GO) analysis of LET-independent up-regulated genes showed that some GO terms were commonly enriched, both 2 hours and 3 weeks after irradiation. GO terms enriched in LET-dependent regulated genes implied that some factor regulates genes that have kinase activity or DNA-binding activity in cooperation with the ATM gene. Of the LET-dependent up-regulated genes, OsPARP3 and OsPCNA were identified, which are involved in DNA repair pathways. This indicates that the Ku-independent alternative non-homologous end-joining pathway may contribute to repairing complex DNA legions induced by high-LET irradiation. These findings may clarify various LET-dependent responses in rice.
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Kotaro
authors.initials: K
authors.lastname: Ishii
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kazama
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Ryouhei
authors.initials: R
authors.lastname: Morita
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.|Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
authors.forename: Tomonari
authors.initials: T
authors.lastname: Hirano
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Tokihiro
authors.initials: T
authors.lastname: Ikeda
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Usuda
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Yoriko
authors.initials: Y
authors.lastname: Hayashi
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Sumie
authors.initials: S
authors.lastname: Ohbu
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Ritsuko
authors.initials: R
authors.lastname: Motoyama
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.affiliation: RIKEN Nishina Center, Wako, Saitama, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Abe
mesh_terms: D004260:DNA Repair; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects*; D020450:Heavy Ions; D018499:Linear Energy Transfer; D012275:Oryza / Q000235:genetics* / Q000528:radiation effects; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins