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191 results on '"Kenmochi, Naoya"'

1. Landscape of driver mutations and their clinical effects on Down syndrome–related myeloid neoplasms

Author

Sato, Tomohiko, Yoshida, Kenichi, Toki, Tsutomu, Kanezaki, Rika, Terui, Kiminori, Saiki, Ryunosuke, Ojima, Masami, Ochi, Yotaro, Mizuno, Seiya, Yoshihara, Masaharu, Uechi, Tamayo, Kenmochi, Naoya, Tanaka, Shiro, Matsubayashi, Jun, Kisai, Kenta, Kudo, Ko, Yuzawa, Kentaro, Takahashi, Yuka, Tanaka, Tatsuhiko, Yamamoto, Yohei, Kobayashi, Akie, Kamio, Takuya, Sasaki, Shinya, Shiraishi, Yuichi, Chiba, Kenichi, Tanaka, Hiroko, Muramatsu, Hideki, Hama, Asahito, Hasegawa, Daisuke, Sato, Atsushi, Koh, Katsuyoshi, Karakawa, Shuhei, Kobayashi, Masao, Hara, Junichi, Taneyama, Yuichi, Imai, Chihaya, Hasegawa, Daiichiro, Fujita, Naoto, Yoshitomi, Masahiro, Iwamoto, Shotaro, Yamato, Genki, Saida, Satoshi, Kiyokawa, Nobutaka, Deguchi, Takao, Ito, Masafumi, Matsuo, Hidemasa, Adachi, Souichi, Hayashi, Yasuhide, Taga, Takashi, Saito, Akiko M., Horibe, Keizo, Watanabe, Kenichiro, Tomizawa, Daisuke, Miyano, Satoru, Takahashi, Satoru, Ogawa, Seishi, and Ito, Etsuro

Published
2024
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2. RNAcentral: a hub of information for non-coding RNA sequences

Author

Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley JF, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, and Williams, Kelly P

Subjects
Biological Sciences, Environmental Sciences, Chemical Sciences, The RNAcentral Consortium, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Published
2019

3. The Role of Alternative mRNA Splicing in Heart Development

Author

Bittel, Douglas C., Kibiryeva, Nataliya, Kenmochi, Naoya, Patil, Prakash, Uechi, Tamayo, Rongish, Brenda, Filla, Mike, Marshall, Jennifer, Artman, Michael, Johnson, Rajasingh, O’Brien, James E., Jr, Nakanishi, Toshio, editor, Baldwin, H. Scott, editor, Fineman, Jeffrey R., editor, and Yamagishi, Hiroyuki, editor

Published
2020
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4. RNAcentral: a comprehensive database of non-coding RNA sequences.

Author

Petrov, Anton, Kay, Simon, Kalvari, Ioanna, Howe, Kevin, Gray, Kristian, Bruford, Elspeth, Kersey, Paul, Cochrane, Guy, Finn, Robert, Bateman, Alex, Kozomara, Ana, Griffiths-Jones, Sam, Frankish, Adam, Zwieb, Christian, Lau, Britney, Williams, Kelly, Chan, Patricia, Lowe, Todd, Cannone, Jamie, Gutell, Robin, Machnicka, Magdalena, Bujnicki, Janusz, Yoshihama, Maki, Kenmochi, Naoya, Chai, Benli, Cole, James, Szymanski, Maciej, Karlowski, Wojciech, Wood, Valerie, Huala, Eva, Berardini, Tanya, Zhao, Yi, Chen, Runsheng, Zhu, Weimin, Paraskevopoulou, Maria, Vlachos, Ioannis, Hatzigeorgiou, Artemis, Ma, Lina, Zhang, Zhang, Puetz, Joern, Stadler, Peter, McDonald, Daniel, Basu, Siddhartha, Fey, Petra, Engel, Stacia, Cherry, J, Volders, Pieter-Jan, Mestdagh, Pieter, Wower, Jacek, Clark, Michael, Quek, Xiu, and Dinger, Marcel

Subjects
Animals, Databases, Nucleic Acid, Genomics, Humans, Nucleotides, RNA, Untranslated, Sequence Analysis, RNA, Species Specificity
Abstract

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Published
2017

9. Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia

Author

Wang, RuNan, Yoshida, Kenichi, Toki, Tsutomu, Sawada, Takafumi, Uechi, Tamayo, Okuno, Yusuke, Sato-Otsubo, Aiko, Kudo, Kazuko, Kamimaki, Isamu, Kanezaki, Rika, Shiraishi, Yuichi, Chiba, Kenichi, Tanaka, Hiroko, Terui, Kiminori, Sato, Tomohiko, Iribe, Yuji, Ohga, Shouichi, Kuramitsu, Madoka, Hamaguchi, Isao, Ohara, Akira, Hara, Junichi, Goi, Kumiko, Matsubara, Kousaku, Koike, Kenichi, Ishiguro, Akira, Okamoto, Yasuhiro, Watanabe, Kenichiro, Kanno, Hitoshi, Kojima, Seiji, Miyano, Satoru, Kenmochi, Naoya, Ogawa, Seishi, and Ito, Etsuro

Published
2015
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23. Phase distribution of spliceosomal introns: implications for intron origin

Author

Yoshihama Maki, Nguyen Hung D, and Kenmochi Naoya

Subjects
Evolution, QH359-425
Abstract

Abstract Background The origin of spliceosomal introns is the central subject of the introns-early versus introns-late debate. The distribution of intron phases is non-uniform, with an excess of phase-0 introns. Introns-early explains this by speculating that a fraction of present-day introns were present between minigenes in the progenote and therefore must lie in phase-0. In contrast, introns-late predicts that the nonuniformity of intron phase distribution reflects the nonrandomness of intron insertions. Results In this paper, we tested the two theories using analyses of intron phase distribution. We inferred the evolution of intron phase distribution from a dataset of 684 gene orthologs from seven eukaryotes using a maximum likelihood method. We also tested whether the observed intron phase distributions from 10 eukaryotes can be explained by intron insertions on a genome-wide scale. In contrast to the prediction of introns-early, the inferred evolution of intron phase distribution showed that the proportion of phase-0 introns increased over evolution. Consistent with introns-late, the observed intron phase distributions matched those predicted by an intron insertion model quite well. Conclusion Our results strongly support the introns-late hypothesis of the origin of spliceosomal introns.

Published
2006
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24. Characteristics and clustering of human ribosomal protein genes

Author

Uechi Tamayo, Washio Takanori, Ishii Kyota, Yoshihama Maki, Kenmochi Naoya, and Tomita Masaru

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism. Results We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG. Conclusion Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.

Published
2006
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25. De Novo Mutations Activating Germline TP53 in an Inherited Bone-Marrow-Failure Syndrome

Author

Toki, Tsutomu, primary, Yoshida, Kenichi, additional, Wang, RuNan, additional, Nakamura, Sou, additional, Maekawa, Takanobu, additional, Goi, Kumiko, additional, Katoh, Megumi C., additional, Mizuno, Seiya, additional, Sugiyama, Fumihiro, additional, Kanezaki, Rika, additional, Uechi, Tamayo, additional, Nakajima, Yukari, additional, Sato, Yusuke, additional, Okuno, Yusuke, additional, Sato-Otsubo, Aiko, additional, Shiozawa, Yusuke, additional, Kataoka, Keisuke, additional, Shiraishi, Yuichi, additional, Sanada, Masashi, additional, Chiba, Kenichi, additional, Tanaka, Hiroko, additional, Terui, Kiminori, additional, Sato, Tomohiko, additional, Kamio, Takuya, additional, Sakaguchi, Hirotoshi, additional, Ohga, Shouichi, additional, Kuramitsu, Madoka, additional, Hamaguchi, Isao, additional, Ohara, Akira, additional, Kanno, Hitoshi, additional, Miyano, Satoru, additional, Kojima, Seiji, additional, Ishiguro, Akira, additional, Sugita, Kanji, additional, Kenmochi, Naoya, additional, Takahashi, Satoru, additional, Eto, Koji, additional, Ogawa, Seishi, additional, and Ito, Etsuro, additional

Published
2018
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28. Identification and characterization of 5α-cyprinol-sulfating cytosolic sulfotransferases (Sults) in the zebrafish (Danio rerio)

Author

Kurogi, Katsuhisa, primary, Yoshihama, Maki, additional, Horton, Austin, additional, Schiefer, Isaac T., additional, Krasowski, Matthew D., additional, Hagey, Lee R., additional, Williams, Frederick E., additional, Sakakibara, Yoichi, additional, Kenmochi, Naoya, additional, Suiko, Masahito, additional, and Liu, Ming-Cheh, additional

Published
2017
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29. Exome sequencing identified RPS15A as a novel causative gene for Diamond-Blackfan anemia

Author

Ikeda, Fumika, Yoshida, Kenichi, Toki, Tsutomu, Uechi, Tamayo, Ishida, Shiori, Nakajima, Yukari, Sasahara, Yoji, Okuno, Yusuke, Kanezaki, Rika, Terui, Kiminori, Kamio, Takuya, Kobayashi, Akie, Fujita, Takashi, Sato-Otsubo, Aiko, Shiraishi, Yuichi, Tanaka, Hiroko, Chiba, Kenichi, Muramatsu, Hideki, Kanno, Hitoshi, Ohga, Shouichi, Ohara, Akira, Kojima, Seiji, Kenmochi, Naoya, Miyano, Satoru, Ogawa, eishi, Ito, Etsuro, Ikeda, Fumika, Yoshida, Kenichi, Toki, Tsutomu, Uechi, Tamayo, Ishida, Shiori, Nakajima, Yukari, Sasahara, Yoji, Okuno, Yusuke, Kanezaki, Rika, Terui, Kiminori, Kamio, Takuya, Kobayashi, Akie, Fujita, Takashi, Sato-Otsubo, Aiko, Shiraishi, Yuichi, Tanaka, Hiroko, Chiba, Kenichi, Muramatsu, Hideki, Kanno, Hitoshi, Ohga, Shouichi, Ohara, Akira, Kojima, Seiji, Kenmochi, Naoya, Miyano, Satoru, Ogawa, eishi, and Ito, Etsuro

Published
2017

31. TBCD may be a causal gene in progressive neurodegenerative encephalopathy with atypical infantile spinal muscular atrophy

Author

Ikeda, Toshio, primary, Nakahara, Akihiko, additional, Nagano, Rie, additional, Utoyama, Maiko, additional, Obara, Megumi, additional, Moritake, Hiroshi, additional, Uechi, Tamayo, additional, Mitsui, Jun, additional, Ishiura, Hiroyuki, additional, Yoshimura, Jun, additional, Doi, Koichiro, additional, Kenmochi, Naoya, additional, Morishita, Shinichi, additional, Nishino, Ichizo, additional, Tsuji, Shoji, additional, and Nunoi, Hiroyuki, additional

Published
2016
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32. Exome sequencing identified RPS15A as a novel causative gene for Diamond-Blackfan anemia

Author

Ikeda, Fumika, primary, Yoshida, Kenichi, additional, Toki, Tsutomu, additional, Uechi, Tamayo, additional, Ishida, Shiori, additional, Nakajima, Yukari, additional, Sasahara, Yoji, additional, Okuno, Yusuke, additional, Kanezaki, Rika, additional, Terui, Kiminori, additional, Kamio, Takuya, additional, Kobayashi, Akie, additional, Fujita, Takashi, additional, Sato-Otsubo, Aiko, additional, Shiraishi, Yuichi, additional, Tanaka, Hiroko, additional, Chiba, Kenichi, additional, Muramatsu, Hideki, additional, Kanno, Hitoshi, additional, Ohga, Shouichi, additional, Ohara, Akira, additional, Kojima, Seiji, additional, Kenmochi, Naoya, additional, Miyano, Satoru, additional, Ogawa, Seishi, additional, and Ito, Etsuro, additional

Published
2016
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33. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes

Author

Yoshihama, Maki, Uechi, Tamayo, Suichi, Asakawa, Kawasaki, Kazuhiko, Kato, Seishi, Kenmochi, Naoya, Shimizu, Nobuyoshi, Tanaka, Tatsuo, Minoshima, Shinsei, Maeda, Noriko, and Higa, Sayomi

Subjects
Ribosomal proteins -- Comparative analysis, Ribosomal proteins -- Research, Genetic research, Health
Abstract

The structure of the genes encoding the human ribosome proteins is described and they are compared with several eukaryotes. Using genomic and full-length cDNA sequences, 73 genes are characterized.

Published
2002

34. [原著］The Structure of Chicken Ribosomal Protein L30

Author

Nakasone, Kaoru, Kenmochi, Naoya, Toku, Seikichi, Tanaka, Tatsuo, and Department of Biochemistry, Faculty of Medicine, UniUersity of the Ryukyus, Okinawa, Japan

Subjects
animal structures, chicken, embryonic structures, cDNA cloning, nucleotide sequence, ribosomal protein L30, amino acid sequence
Abstract

The primary structure of the chicken ribosomal protein L30 was deduced from the sequence of nucleotide in a recombinant cDNA. Chicken ribosomal protein L30 has 115 amino acids and a molecular weight of 12,814 including initiator methionine. Hybridization of the cCDNA to the restriction enzyme digests of chicken liver DNA suggests that L30 gene is a single copy. Chicken L30 is homologous to ribosomal proteins from other eukaryotes and archaebacteria but not to those from eubacteria.

Published
1994

38. Loss of function mutations inRPL27andRPS27identified by whole-exome sequencing in Diamond-Blackfan anaemia

Author

Wang, RuNan, primary, Yoshida, Kenichi, additional, Toki, Tsutomu, additional, Sawada, Takafumi, additional, Uechi, Tamayo, additional, Okuno, Yusuke, additional, Sato-Otsubo, Aiko, additional, Kudo, Kazuko, additional, Kamimaki, Isamu, additional, Kanezaki, Rika, additional, Shiraishi, Yuichi, additional, Chiba, Kenichi, additional, Tanaka, Hiroko, additional, Terui, Kiminori, additional, Sato, Tomohiko, additional, Iribe, Yuji, additional, Ohga, Shouichi, additional, Kuramitsu, Madoka, additional, Hamaguchi, Isao, additional, Ohara, Akira, additional, Hara, Junichi, additional, Goi, Kumiko, additional, Matsubara, Kousaku, additional, Koike, Kenichi, additional, Ishiguro, Akira, additional, Okamoto, Yasuhiro, additional, Watanabe, Kenichiro, additional, Kanno, Hitoshi, additional, Kojima, Seiji, additional, Miyano, Satoru, additional, Kenmochi, Naoya, additional, Ogawa, Seishi, additional, and Ito, Etsuro, additional

Published
2014
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44. Characteristics and clustering of human ribosomal protein genes

Author

Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, Tomita, Masaru, Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, and Tomita, Masaru

Abstract

Background: The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins （RPs）. The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism. Results: We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that （1） most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection （LND）, and fetal brain. However, 17 genes, including the P protein genes （RPLP0, RPLP1, RPLP2）, are expressed in a tissue-specific manner. （2） Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. （3） Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. （4） The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG. Conclusion: Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.

Published
2006

46. TBCDmay be a causal gene in progressive neurodegenerative encephalopathy with atypical infantile spinal muscular atrophy

Author

Ikeda, Toshio, Nakahara, Akihiko, Nagano, Rie, Utoyama, Maiko, Obara, Megumi, Moritake, Hiroshi, Uechi, Tamayo, Mitsui, Jun, Ishiura, Hiroyuki, Yoshimura, Jun, Doi, Koichiro, Kenmochi, Naoya, Morishita, Shinichi, Nishino, Ichizo, Tsuji, Shoji, and Nunoi, Hiroyuki

Abstract

Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder caused by survival motor neuron gene mutations. Variant forms of SMA accompanied by additional clinical presentations have been classified as atypical SMA and are thought to be caused by variants in as yet unidentified causative genes. Here, we presented the clinical findings of two siblings with an SMA variant followed by progressive cerebral atrophy, and the results of whole-exome sequencing analyses of the family quartet that was performed to identify potential causative variants. We identified two candidate homozygous missense variants, R942Q in the tubulin-folding cofactor D(TBCD) gene and H250Q in the bromo-adjacent homology domain and coiled-coil containing 1(BAHCC1) gene, located on chromosome 17q25.3 with an interval of 1.4 Mbp. The in silicoanalysis of both variants suggested that TBCDrather than BAHCC1was likely the pathogenic gene (TBCDsensitivity, 0.68; specificity, 0.97; BAHCC1sensitivity, 1.00; specificity, 0.00). Thus, our results show that TBCDis a likely novel candidate gene for atypical SMA with progressive cerebral atrophy. TBCDis predicted to have important functions on tubulin integrity in motor neurons as well as in the central nervous system.

Published
2017
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49. The NPC Motif of Aquaporin-11, Unlike the NPA Motif of Known Aquaporins, Is Essential for Full Expression of Molecular Function

Author

Ikeda, Masahiro, primary, Andoo, Ayaka, additional, Shimono, Mariko, additional, Takamatsu, Natsuko, additional, Taki, Asaka, additional, Muta, Kanako, additional, Matsushita, Wataru, additional, Uechi, Tamayo, additional, Matsuzaki, Toshiyuki, additional, Kenmochi, Naoya, additional, Takata, Kuniaki, additional, Sasaki, Sei, additional, Ito, Katsuaki, additional, and Ishibashi, Kenichi, additional

Published
2011
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