Papers - Kanai, Akio

A screening system for artificial small RNAs that inhibit the growth of Escherichia coli

Mizuki Komasa, Kosuke Fujishima, Kiriko Hiraoka, Atsuko Shinhara, Baek-Seok Lee, Masaru Tomita and Akio Kanai

The Journal of Biochemistry 150 ( 3 ) 289-294 2011.09

Research paper (scientific journal), Joint Work, Accepted

Vertebrate-virus-encoded microRNAs and their sequence conservation

Takane, K. and Kanai, A.

Japanese Journal of Infectious Diseases 64 ( 5 ) 357-366 2011.09

Research paper (scientific journal), Joint Work, Accepted

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.

Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H. and Kanai, A.

BMC Genomics (BioMed Central)  12   428 2011.08

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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Background
In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.

Results
We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.

Conclusions
This comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.

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Systems biology reveals microRNA-mediated gene regulation

Watanabe, Y. and Kanai, A.

Frontiers in Genetics 2   29 2011.06

Research paper (scientific journal), Joint Work, Accepted

tRNADB-CE 2011: tRNA gene database curated manually by experts.

Abe, T., Ikemura, T., Sugahara, J., Kanai, A., Ohara, Y., Uehara, H., Kinouchi, M., Kanaya, S., Yamada, Y., Muto, A. and Inokuchi, H.

Nucleic Acids Research 39   D210-D213 2011

Research paper (scientific journal), Joint Work, Accepted

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

Takuro Nunoura, Yoshihiro Takaki, Jungo Kakuta, Shinro Nishi, Junichi Sugahara, Hiromi Kazama, Gab-Joo Chee, Masahira Hattori, Akio Kanai, Haruyuki Atomi, Ken Takai and Hideto Takami

Nucleic Acids Research 39 ( 8 ) 3204-3223 2011

Research paper (scientific journal), Joint Work, Accepted

Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes

Rintaro Saito, Keisuke Kohno, Yuki Okada, Yuko Osada, Koji Numata, Chihiro Kohama, Kazufumi Watanabe, Hajime Nakaoka, Naoyuki Yamamoto, Akio Kanai, Hiroshi Yasue, Soichiro Murata, Kuniya Abe, Masaru Tomita, Nobuhiro Ohkohchi, Hidenori Kiyosawa

BMC Medical Genomics 4   42 2011

Research paper (scientific journal), Joint Work

Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain

Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A.

Molecular Biology and Evolution (Oxford Academic)  27 ( 10 ) 2233 - 2243 2010.10

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

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Recently, diverse arrangements of transfer RNA (tRNA) genes have been found in the domain Archaea, in which the tRNA is interrupted by a maximum of three introns or is even fragmented into two or three genes. Whereas most of the eukaryotic tRNA introns are inserted strictly at the canonical nucleotide position (37/38), archaeal intron-containing tRNAs have a wide diversity of small tRNA introns, which differ in their numbers and locations. This feature is especially pronounced in the archaeal order Thermoproteales. In this study, we performed a comprehensive sequence comparison of 286 tRNA introns and their genes in seven Thermoproteales species to clarify how these introns have emerged and diversified during tRNA gene evolution. We identified 46 intron groups containing sets of highly similar sequences (>70%) and showed that 16 of them contain sequences from evolutionarily distinct tRNA genes. The phylogeny of these 16 intron groups indicates that transposition events have occurred at least seven times throughout the evolution of Thermoproteales. These findings suggest that frequent intron transposition occurs among the tRNA genes of Thermoproteales. Further computational analysis revealed limited insertion positions and corresponding amino acid types of tRNA genes. This has arisen because the bulge–helix–bulge splicing motif is required at the newly transposed position if the pre-tRNA is to be correctly processed. These results clearly demonstrate a newly identified mechanism that facilitates the late gain of short introns at various noncanonical positions in archaeal tRNAs.

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Transcription-associated mutagenesis increase protein sequence diversity more effectively than does random mutagenesis in Escherichia coli

Kim, H., Lee, B.-S., Tomita, M. and Kanai, A.

PLoS ONE 5 ( 5 ) e10567 2010.05

Research paper (scientific journal), Joint Work, Accepted

Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes.

Maruyama, S., Sugahara, J., Kanai, A. and Nozaki, H.

Molecular Biology and Evolution 27 ( 5 ) 1070-1076 2010.05

Research paper (scientific journal), Joint Work, Accepted

Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals

Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M. and Kanai, A.

BMC Genomics 11 ( 101 )  2010.02

Research paper (scientific journal), Joint Work, Accepted

Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus

Sayaka Kitamura, Kosuke Fujishima, Asako Sato, Daisuke Tsuchiya, Masaru Tomita and Akio Kanai

Biochemical Journal 426 ( 3 ) 337-344 2010.01

Research paper (scientific journal), Joint Work, Accepted

Disrupted tRNA gene diversity and possible evolutionary scenarios

Sugahara, J., Fujishima, K., Morita, K., Tomita, M. and Kanai, A.

Journal of Molecular Evolution 69 ( 5 ) 497-504 2009.10

Research paper (scientific journal), Joint Work, Accepted

Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes

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.

BMC Genomics 10   392 2009.08

Research paper (scientific journal), Joint Work, Accepted

Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order Thermoproteales

Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A.

Molecular Biology and Evolution 25 ( 12 ) 2709-2716 2008.10

Research paper (scientific journal), Joint Work, Last author, Corresponding author, Accepted

Sequence evidence in the archaeal genome that tRNAs emerged through the combination of ancestral genes as 5’ and 3’ tRNA halves

Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A.

PLoS ONE 3 ( 2 ) e1622 2008.02

Research paper (scientific journal), Joint Work, Accepted

Comparative expression analysis uncovers novel features of endogenous antisense transcription

Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A, Abe K, Tomita M, Kiyosawa H.

Human Molecular Genetics 17 ( 11 ) 1631-1640 2008.02

Research paper (scientific journal), Joint Work, Accepted

Perspective in the evolution of human microRNAs: copy number expansion and acquisition of target gene specialization

Watanabe, Y., Tomita, M. and Kanai, A

Progress of Theoretical Physics Supplement 173   219-228 2008

Research paper (scientific journal), Joint Work, Accepted

Comparison and characterization of proteomes in the three domains of life using 2D correlation analysis

Fujishima, K., Komasa, M., Kitamura, S., Tomita, M. and Kanai, A

Progress of Theoretical Physics Supplement 173   206-218 2008

Research paper (scientific journal), Joint Work, Accepted

A novel processing pathway via a circular RNA intermediate of permutated tRNA genes in Cyanidioschyzon merolae

Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y.

Science 318   450-453 2007.10

Research paper (scientific journal), Joint Work, Accepted