RIKEN Accel. Prog. Rep. 50 (2017)

Ⅰ. HIGHLIGHTS OF THE YEAR

Change in rice gene expression profile dependent on linear energy transfer
after heavy-ion beam irradiation†
K. Ishii,䠆1 Y. Kazama,䠆1 R. Morita,䠆1 T. Hirano,䠆1,*2 T. Ikeda,䠆1 S. Usuda,䠆1 Y. Hayashi,䠆1 S. Ohbu,䠆1 R. Motoyama,䠆3Y. Nagamura,䠆3 and T. Abe䠆1
LET is an important factor affecting several aspects of
the irradiation effect, such as cell survival and mutation
frequency.1) The effect of LET on deletion induction
increases up to an LET value of approximately 100keV/ȝm2) while the mutation frequency increases abruptlyand peaks at a particular LET value.1) The mechanism
between LET and the corresponding mutation frequency is
still unknown. In this study, we focused on the effect ofLET on gene expression profiles.
Oryza sativa L. cv. µ1LSSRQEDUH¶VHHGVZHUe imbibed for
3 days. The seeds were irradiated with 22.5 or 50 keV/ȝm Cions or with 63 or 80 keV/ȝm Ne ions at a dose of 15 Gy.
Embryos were sampled 2 h after irradiation. Gene
expression profiles were generated using a rice 4×44K
microarray RAP-DB (Agilent Technologies, Tokyo, Japan).

We defined 379 genes showing a significant change inexpression level (FC > 2, and p < 0.05) at all four LETs as³LET-independent up-regulated genes´ and 628 genes
showing a significant change in expression level at an LETof 80 keV/ȝPEXWQRWDWNH9/ȝPDV³LET-dependent
up-regulated genes´. A singular enrichment analysis (SEA)
using a gene ontology (GO) analysis toolkit agriGO
revealed that GO terms significantly S   enrichedwere different in LET-dependent up-regulated genes and
LET-independent up-regulated genes (Fig. 1), which
implies that some specific genetic pathway is induced
depending on the complexity of DNA damage.
Additionally, OsPCNA and OsPARP3 were found to be
LET-dependent up-regulated genes (Fig 2). Althoughmolecular functions of rice PARP family genes are largely
unknown, some of them are involved in Ku-independent
non homologous end joining (A-NHEJ) with Xrcc1 andDNA ligase III in animals3) and plants.4) OsPCNA forms acomplex with OsXRCC1 in vivo.5) We assume that the highexpression of OsPARP3 and OsPCNA is needed to repair
the high-LET induced DNA lesions via Ku-independent
NHEJ.
In this study, we found an LET-dependent change of gene
expression profile, which is a clue to the clarification of therelationship between LET and mutation frequency.

Fig 2. Response of OsPCNA and OsPARP3 gene
expressions to heavy-ion beam irradiation. Fold changes inexpression level of OsPCNA (A) and OsPARP3 (B)compared to the unirradiated control are shown. *: p < 0.05
(6WXGHQW¶VW-test).

Fig 1. SEA analysis. The horizontal axis shows thedistribution of the GO term, which is a percentage of genes
having each GO term in the analyzed gene set. Blue, red,
and white boxes indicate the distribution of
LET-independent up-regulated genes, LET-dependent
up-regulated genes, and whole genes (rice TIGR locus).

References
1) Y. Kazama et al., Plant Biotechnol. 25(1)113 (2008).
2) A. Ottolenghi et al., Radiat. Environ. Biophys. 34(4)239 (1995).
3) C. Charbonnel et al., Plant J. 64(2)280 (2010).
4) Q. Jia et al., Plant Mol. Biol. 82(4-5)339 (2013).
5) Y. Uchiyama et al., Planta 227(6)1233 (2008).

 Condensed from the article in PLoS ONE 11(7):e0160061 (2016)
RIKEN Nishina Center
䠆2
Faculty of Agriculture, University of Miyazaki
䠆3Agrogenomics Research Center, National Institute of AgrobiologicalSciences
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