2012

○  Hamashima, K., Fujishima, K., Masuda, T., Sugahara, J., Tomita, M. and Kanai, A. (2012) Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Research in press.

○  Murakami, S., Fujishima, K., Tomita, M. and Kanai, A. (2012) Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and Environmental Microbiology 78(4): 1015-1022.

○  Sugahara, J., Fujishima, K., Nunoura, T., Takaki, Y., Takami, H., Takai, K., Tomita, M. and Kanai, A. (2012) Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS ONE in press.

2011

○  Fujishima, K., Sugahara, J., Miller, CS., Baker BJ., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, JF. and Kanai, A. (2011) A novel three-unit tRNA splicing endonuclease found in ultrasmall archaea possesses broad substrate specificity. Nucleic Acids Research 39(22): 9695-9704.

○  Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M. and Kanai, A. (2011) GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes to Cells 16: 1190-1199.

○  Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H. and Kanai, A. (2011) Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 12: 428.

○  Komasa, M., Fujishima, K., Hiraoka, K., Shinhara, A., Lee, B.-S., Tomita, M. and Kanai, A. (2011) A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. The Journal of Biochemistry 150(3): 289-294.

○  Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., Chee, G.-J., Hattori, M., Kanai, A., Atomi, H., Takai, K. and Takami, H. (2011) Insights into the evolution of archaea and eukaryotic protein modifier systems reveled by the genome of a novel archaeal group. Nucleic Acids Research 39 (8): 3204-3223.

○  Abe, T., Ikemura, T., Sugahara, J., Kanai, A., Ohara, Y., Uehara, H., Kinouchi, M., Kanaya, S., Yamada, Y., Muto, A. and Inokuchi, I. (2011) tRNADB-CE 2011: tRNA gene database curated manually by experts. Nucleic Acids Research 39: D210-D213.

○  Saito, R., Kohno, K., Okada, Y., Osada, Y., Numata, K., Kohama, C., Watanabe, K., Nakaoka, H., Yamamoto, N., Kanai, A., Yasue, H., Murata, S., Abe, K., Tomita, M., Ohkohchi, N. and Kiyosawa, H. (2011) Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Medical Genomics 4: 42.

○  Watanabe, Y. and Kanai, A. (2011) Systems biology reveals microRNA-mediated gene regulation. Frontiers in Genetics 2: 29. Review

○  Takane, K. and Kanai, A. (2011) Vertebrate-virus-encoded microRNAs and their sequence conservation. Japanese Journal of Infectious Diseases 64(5): 357-366. Invited Review

○  Fujishima, K. and Kanai, A. (2011) Diversity, function and processing of archaeal non-coding RNAs. in “Archaea: Structure, Habitats and Ecological Significance” Nova Science Publishers, Inc. New York. pp. 69-94. Review

2010

○  Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A. (2010) Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Molecular Biology and Evolution 27(10): 2233-2243.

○  Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M. and Kanai, A. (2010) Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics 11: 101.

○  Maruyama, S., Sugahara, J., Kanai, A. and Nozaki, H. (2010) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Molecular Biology and Evolution 27(5): 1070-1076.

○  Kitamura, S., Fujishima, K., Sato, A., Tsuchiya, D., Tomita, M. and Kanai, A. (2010) Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus. Biochemical Journal 426: 337-344.

○  Kim, H., Lee, B.-S., Tomita, M. and Kanai, A. (2010) Transcription-associated mutagenesis increase protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PLoS ONE 5(5): e10567.

2009

○  Kanai, A., Sato, A., Fukuda, Y. Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G. and Tomita, M. (2009) Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus.  RNA 15(3): 420-431.

○  Fujishima, K., Sugahara, J., Kikuta, K., Hirano, R., Sato, A., Tomita, M. and Kanai, A. (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proceedings of the National Academy of Sciences. U. S. A. 106(8): 2683-2687.

○  Numata, K., Osada, Y., Okada, Y., Saito, R., Hiraiwa, N., Nakaoka, H., Yamamoto, N., Watanabe, K., Okubo, K., Kohama, C., Kanai, A., Abe, K. and Kiyosawa, H. (2009) Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes. BMC Genomics 10: 392.

○  Sugahara, J., Fujishima, K., Morita, K., Tomita, M. and Kanai, A. (2009) Disrupted tRNA gene diversity and possible evolutionary scenarios. Journal of Molecular Evolution 69: 497-504. Review

Selected Previous Papers:

○  Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A. (2008) Comprehensive analysis of archaeal tRNA reveals rapid increase of tRNA introns in the order Thermoproteales. Molecular Biology and Evolution 25(12): 2709-2716.

○  Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H. and Tomita, M. (2007) Multiple high throughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597.  

○  Fujishima, K., Komasa, M., Kitamura, S., Suzuki, H., Tomita, M. and Kanai, A. (2007) Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in hyperthermophilic archeaon Pyrococcus furiosus. DNA Research 14: 91-102.

○  Kochiwa, H., Tomita, M. and Kanai, A. (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evolutionary Biology 7:128.

○  Watanabe, Y., Tomita, M. and Kanai, A. (2007) Computational method for microRNA target prediction. Methods in Enzymology 427: 65-86. Review

○  Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y. (2007) A novel processing pathway via a circular RNA intermediate of permutated tRNA genes in Cyanidioschyzon merolae. Science 318: 450-453.

○  Kanai, A., Sato, A., Imoto, J. and Tomita, M. (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. Biochemical Journal 393: 373-379.

○  Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., RIKEN GER Group Members, Hayashizaki, Y. and Tomita, M. (2003) Identification of putative non-coding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research 13: 1301-1306.

○  Kanai, A., Oida, H., Matsuura, N. and Doi, H. (2003) Expression cloning and characterization of   a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochemical Journal 372: 253-261.

(1)  Frontiers in Non-coding RNA, Associate Editor

http://www.frontiersin.org/non-coding_rna

(2)  Frontiers in Virology, Review Editor

(3) PLoS ONE, Academic Editor