Updated on 2022/05/22

写真a

 
OSATO, Naoki
 
Affiliation
Faculty of Science and Engineering, Waseda Research Institute for Science and Engineering
Job title
Researcher(Assistant Professor)

Professional Memberships

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    International Society of Computational Biology

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    INFORMATION PROCESSING SOCIETY OF JAPAN

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    THE GENETICS SOCIETY OF JAPAN

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    THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

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    JAPANESE SOCIETY FOR BIOINFORMATICS

 

Research Areas

  • System genome science

  • Life, health and medical informatics

Research Interests

  • Biochemistry

  • Molecular biology

  • Informatics

  • Statistics

  • Genome science

  • Computational biology

  • Bioinformatics

  • Chromatin interaction

  • Sense-antisense mRNA

  • Non-protein-coding RNA

  • Epigenome

  • Transcription factor

  • Gene expression

  • Transcriptonal cascade

  • Transcriptional regulation

▼display all

Papers

  • Discovery of directional chromatin-associated regulatory motifs affecting human gene transcription

    Naoki Osato

       2020.10

    　View Summary

    <title>Abstract</title><sec><title>Background</title>Chromatin interactions are essential in enhancer-promoter interactions (EPIs) and transcriptional regulation. CTCF and cohesin proteins located at chromatin interaction anchors and other DNA-binding proteins such as YY1, ZNF143, and SMARCA4 are involved in chromatin interactions. However, there is still no good overall understanding of proteins associated with chromatin interactions and insulator functions.

    </sec><sec><title>Results</title>Here, I describe a systematic and comprehensive approach for discovering DNA-binding motifs of transcription factors (TFs) that affect EPIs and gene expression. This analysis identified 96 biased orientations [64 forward-reverse (FR) and 52 reverse-forward (RF)] of motifs that significantly affected the expression level of putative transcriptional target genes in monocytes, T cells, HMEC, and NPC and included CTCF, cohesin (RAD21 and SMC3), YY1, and ZNF143; some TFs have more than one motif in databases; thus, the total number is smaller than the sum of FRs and RFs. KLF4, ERG, RFX, RFX2, HIF1, SP1, STAT3, and AP1 were associated with chromatin interactions. Many other TFs were also known to have chromatin-associated functions. The predicted biased orientations of motifs were compared with chromatin interaction data. Correlations in expression level of nearby genes separated by the motif sites were then examined among 53 tissues.

    </sec><sec><title>Conclusion</title>One hundred FR and RF orientations associated with chromatin interactions and functions were discovered. Most TFs showed weak directional biases at chromatin interaction anchors and were difficult to identify using enrichment analysis of motifs. These findings contribute to the understanding of chromatin-associated motifs involved in transcriptional regulation, chromatin interactions/regulation, and histone modifications.

    </sec>

    DOI

  • Glycerol kinase stimulates uncoupling protein 1 expression by regulating fatty acid metabolism in beige adipocytes.

    Mari Iwase, Soshi Tokiwa, Shigeto Seno, Takako Mukai, Yu-Sheng Yeh, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Sigenobu Matsumura, Tatsuya Kusudo, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

    The Journal of biological chemistry   295 ( 20 ) 7033 - 7045  2020.05  [Refereed]  [International journal]

    　View Summary

    Browning of adipose tissue is induced by specific stimuli such as cold exposure and consists of up-regulation of thermogenesis in white adipose tissue. Recently, it has emerged as an attractive target for managing obesity in humans. Here, we performed a comprehensive analysis to identify genes associated with browning in murine adipose tissue. We focused on glycerol kinase (GYK) because its mRNA expression pattern is highly correlated with that of uncoupling protein 1 (UCP1), which regulates the thermogenic capacity of adipocytes. Cold exposure-induced Ucp1 up-regulation in inguinal white adipose tissue (iWAT) was partially abolished by Gyk knockdown (KD) in vivo Consistently, the Gyk KD inhibited Ucp1 expression induced by treatment with the β-adrenergic receptors (βAR) agonist isoproterenol (Iso) in vitro and resulted in impaired uncoupled respiration. Gyk KD also suppressed Iso- and adenylate cyclase activator-induced transcriptional activation and phosphorylation of the cAMP response element-binding protein (CREB). However, we did not observe these effects with a cAMP analog. Therefore Gyk KD related to Iso-induced cAMP products. In Iso-treated Gyk KD adipocytes, stearoyl-CoA desaturase 1 (SCD1) was up-regulated, and monounsaturated fatty acids such as palmitoleic acid (POA) accumulated. Moreover, a SCD1 inhibitor treatment recovered the Gyk KD-induced Ucp1 down-regulation and POA treatment down-regulated Iso-activated Ucp1 Our findings suggest that Gyk stimulates Ucp1 expression via a mechanism that partially depends on the βAR-cAMP-CREB pathway and Gyk-mediated regulation of fatty acid metabolism.

    DOI PubMed

  • Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes.

    Mari Iwase, Shoko Sakai, Shigeto Seno, Yu-Sheng Yeh, Tony Kuo, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Paul Horton, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

    Bioscience, biotechnology, and biochemistry   84 ( 2 ) 305 - 313  2020.02  [Refereed]  [International journal]

    　View Summary

    Specific conditions, such as exposure to cold, can induce the production of brown-like adipocytes in white adipose tissue. These adipocytes express high levels of uncoupling protein 1 (UCP1) and energy expended by generating heat. Thus, these are a potential target for the prevention or treatment of obesity. The present study involved a comprehensive analysis of the adipose tissue to understand the relationship between long non-coding RNA (lncRNA) 2310069B03Rik and UCP1. Cold exposure increased both lncRNA 2310069B03Rik and Ucp1 expression in inguinal white adipose tissue (iWAT). However, overexpression of lncRNA 2310069B03Rik suppressed the Ucp1 mRNA expression and the promoter activity of UCP1 in the iWAT primary adipocytes. In addition, compared to the early induction of Ucp1 expression by cold stimulation, the induction of lncRNA 2310069B03Rik expression was later. These results suggest that lncRNA 2310069B03Rik functions as a suppression factor of Ucp1 expression.

    DOI PubMed

  • Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells.

    Ryuichiro Nakato, Youichiro Wada, Ryo Nakaki, Genta Nagae, Yuki Katou, Shuichi Tsutsumi, Natsu Nakajima, Hiroshi Fukuhara, Atsushi Iguchi, Takahide Kohro, Yasuharu Kanki, Yutaka Saito, Mika Kobayashi, Akashi Izumi-Taguchi, Naoki Osato, Kenji Tatsuno, Asuka Kamio, Yoko Hayashi-Takanaka, Hiromi Wada, Shinzo Ohta, Masanori Aikawa, Hiroyuki Nakajima, Masaki Nakamura, Rebecca C McGee, Kyle W Heppner, Tatsuo Kawakatsu, Michiru Genno, Hiroshi Yanase, Haruki Kume, Takaaki Senbonmatsu, Yukio Homma, Shigeyuki Nishimura, Toutai Mitsuyama, Hiroyuki Aburatani, Hiroshi Kimura, Katsuhiko Shirahige

    Epigenetics & chromatin   12 ( 1 ) 77 - 77  2019.12  [Refereed]  [International journal]

    　View Summary

    BACKGROUND: Endothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phenotypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from different organs are not well understood. RESULTS: To characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome-wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identified 3765 EC-specific enhancers, some of which were associated with disease-associated genetic variations. We also identified various candidate marker genes for each EC type. We found that the nine EC types can be divided into two subgroups, corresponding to those with upper-body origins and lower-body origins, based on their epigenomic landscape. Epigenomic variations were highly correlated with gene expression patterns, but also provided unique information. Most of the deferentially expressed genes and enhancers were cooperatively enriched in more than one EC type, suggesting that the distinct combinations of multiple genes play key roles in the diverse phenotypes across EC types. Notably, many homeobox genes were differentially expressed across EC types, and their expression was correlated with the relative position of each organ in the body. This reflects the developmental origins of ECs and their roles in angiogenesis, vasculogenesis and wound healing. CONCLUSIONS: This comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.

    DOI PubMed

  • Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity

    Sharma A, Osato N, Liu H, Asthana S, Dakal TC, Ambrosini G, Bucher P, Schmit I, Wullmer U

    Scientific Report   9 ( 18464 )  2019  [Refereed]

    DOI

  • Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads

    Sota Y, Seno S, Shigeta H, Osato N, Shimoda M, Noguchi S, Matsuda H

    Journal of Bioinformatics and Computational Biology   17 ( 03 ) 1940008 - 1940008  2019  [Refereed]  [International journal]

    　View Summary

    Fusion genes are involved in cancer, and their detection using RNA-Seq is insufficient given the relatively short reading length. Therefore, we proposed a shifted short-read clustering (SSC) method, which focuses on overlapping reads from the same loci and extends them as a representative sequence. To verify their usefulness, we applied the SSC method to RNA-Seq data from four types of cell lines (BT-474, MCF-7, SKBR-3, and T-47D). As the slide width of the SSC method increased to one, two, five, or ten bases, the read length was extended from 201 bases to 217 (108%), 234 (116%), 282 (140%), or 317 (158%) bases, respectively. Furthermore, fusion genes were investigated using STAR-Fusion, a fusion gene detection tool, with and without the SSC method. When one base was shifted by the SSC method, the reads mapped to multiple loci decreased from 9.7% to 4.6%, and the sensitivity of the fusion gene was improved from 47% to 54% on average (BT-474: from 48% to 57%, MCF-7: 49% to 53%, SKBR-3: 50% to 57%, and T-47D: 43% to 50%) compared with original data. When the reads are shifted more, the positive predictive value was also improved. The SSC method could be an effective method for fusion gene detection.

    DOI PubMed

  • The DPP-4 inhibitor, teneligliptin enhances brown adipose tissue function, leading to the prevention of obesity in mice

    Takeda K, Sawazaki H, Takahashi H, Yeh YS, Jheng HF, Nomura W, Ara T, Takahashi N, Seno S, Osato N, Matsuda H, Kawata T, Goto T

    FEBS Open Bio    2018.07  [Refereed]

    DOI

  • Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

    Naoki Osato

    BMC Genomics   19 ( 957 )  2018.01  [Refereed]

    　View Summary

    Background: Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Results: Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Conclusions: Human putative transcriptional target genes showed significant functional enrichments. Functional enrichments were related to the cellular functions. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.

    DOI

  • Detection of Fusion Genes from Human Breast Cancer Cell-line RNA-Seq Data Using Shifted Short Read Clustering

    Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzaburo Noguchi, Hideo Matsuda

    PROCEEDINGS 2018 IEEE 18TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE)     159 - 162  2018

    　View Summary

    Fusion genes make for one of the mechanisms of tumorigenesis. The identification of fusion genes by RNA-Seq has attracted attention. Various methods for detecting fusion genes have been proposed, but their accuracy is not sufficient. One of the causes of this problem is the relatively short reading length in RNA-Seq data. Therefore, before mapping RNA-Seq data, we proposed a method, which is based on shifted short-read clustering (SSC), to identify shifted reads of the same origin and extend them as representative sequences. As a result, we assumed that the percentage of uniquely mapped reads would be increased, and the detection rates of the fusion genes could be improved. To verify these hypotheses, we applied the SSC method to RNA-Seq data from three cell-lines (BT-474, MCF-7, and SKBR-3). When only one base was shifted, the average read lengths of BT-474, MCF-7, and SKBR-3 were extended from 201 to 223 bases (111%), 201 to 214 bases (106%), and 201 to 213 bases (106%), respectively. Furthermore, the effectiveness of the SSC method is demonstrated by comparing the performances of a fusion gene detection tool's results, STAR-Fusion, with and without the SSC method of the reads. The percentage of uniquely mapped reads of BT-474, MCF-7, and SKBR-3 were improved from 88% to 93%, 88% to 94%, and 92% to 95%, respectively. Finally, the fusion gene detection rates of BT-474, MCF-7, and SKBR-3 were increased from 48% to 57%, 49% to 53%, and 50% to 53% respectively. The SSC method is considered to be an effective method not only for improving the percentage of uniquely mapped reads but also for fusion gene detection.

    DOI

  • Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

    Naoki Osato

      2017-BIO-52(1)   1 - 6  2017.11  [Refereed]

  • Transcription factor IRF8 plays a critical role in the development of murine basophils and mast cells

    Haruka Sasaki, Daisuke Kurotaki, Naoki Osato, Hideaki Sato, Izumi Sasaki, Shin-ichi Koizumi, Hongsheng Wang, Chika Kaneda, Akira Nishiyama, Tsuneyasu Kaisho, Hiroyuki Aburatani, Herbert C. Morse, Keiko Ozato, Tomohiko Tamura

    BLOOD   125 ( 2 ) 358 - 369  2015.01  [Refereed]

    　View Summary

    Basophils and mast cells play critical roles in host defense against pathogens and allergic disorders. However, the molecular mechanism by which these cells are generated is not completely understood. Here we demonstrate that interferon regulatory factor-8 (IRF8), a transcription factor essential for the development of several myeloid lineages, also regulates basophil and mast cell development. irf8(-/-) mice displayed a severe reduction in basophil counts, which was accounted for by the absence of pre-basophil and mast cell progenitors (pre-BMPs). Although Irf8(-/-) mice retained peripheral tissue mast cells, remaining progenitors from mice including granulocyte progenitors (GPs) were unable to efficiently generate either basophils or mast cells, indicating that IRF8 also contributes to the development of mast cells. IRF8 appeared to function at the GP stage, because IRF8 was expressed in GPs, but not in basophils, mast cells, and basophi/mast cell-restricted progenitor cells. Furthermore, we demonstrate that GATA2, a transcription factor known to promote basophil and mast cell differentiation, acts downstream of IRF8. These results shed light on the pathways and mechanism underlying the development of basophils and mast cells.

    DOI PubMed

  • Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation

    Daisuke Kurotaki, Naoki Osato, Akira Nishiyama, Michio Yamamoto, Tatsuma Ban, Hideaki Sato, Jun Nakabayashi, Marina Umehara, Noriko Miyake, Naomichi Matsumoto, Masatoshi Nakazawa, Keiko Ozato, Tomohiko Tamura

    BLOOD   121 ( 10 ) 1839 - 1849  2013.03  [Refereed]

    　View Summary

    Monocytes regulate host defenses, inflammation, and tissue homeostasis. The transcription factor interferon regulatory factor-8 (IRF8) stimulates monocyte/macrophage differentiation, yet genome-wide understanding of the differentiation program initiated by IRF8 is lacking. By combining chromatin immunoprecipitation sequencing with gene expression profiling, we show that during IRF8-dependent monocyte differentiation, IRF8 binding occurs at both promoter-proximal and promotor-distal regions together with the transcription factor PU.1 and is associated with gene induction. Many of the promoter-distal IRF8 binding sites show an increase in histone H3 lysine 4 monomethylation, a signature for enhancers. However, about half the IRF8-induced genes were not bound by IRF8, suggesting the involvement of downstream transcription factors. Analysis of DNA motifs in cis-regulatory elements of these indirect IRF8 target genes predicted that Kruppel-like factor-4 (KLF4)-essential for Ly6C(+) monocyte development-is one such factor. Indeed, monocyte development in Irf8(-/-) mice is as defective as that in Klf4(-/-) chimeric mice. Moreover, Irf8(-/-) monocyte-dendritic cell progenitors do not express Klf4 messenger RNA. Introduction of KLF4 into an Irf8(-/-) myeloid progenitor cell line induced a subset of IRF8 target genes and caused partial monocyte differentiation. Taken together, our present results uncover genome-wide behavior of IRF8 and identify an IRF8-KLF4 axis that operates during monocyte differentiation.

    DOI PubMed

  • Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex

    Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua J. Zhu, M. Inmaculada Barrasa, Melissa M. Harrison, H. Robert Horvitz, Albertha J. M. Walhout, Kirsten A. Hagstrom

    PLOS GENETICS   7 ( 5 )  2011.05  [Refereed]

    　View Summary

    DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54. We show that LIN-54 DNA-binding activity recruits DRM to promoters enriched for adjacent putative E2F/DP and LIN-54 binding sites, suggesting that these two DNA-binding moieties together direct DRM to its target genes. Chromatin immunoprecipitation and gene expression profiling reveals conserved roles for DRM in regulating genes involved in cell division, development, and reproduction. We find that LIN-54 promotes expression of reproduction genes in the germline, but prevents ectopic activation of germline-specific genes in embryonic soma. Strikingly, C. elegans DRM does not act uniformly throughout the genome: the DRM recruitment motif, DRM binding, and DRM-regulated embryonic genes are all under-represented on the X chromosome. However, germline genes down-regulated in lin-54 mutants are over-represented on the X chromosome. We discuss models for how loss of autosome-bound DRM may enhance germline X chromosome silencing. We propose that autosome-enriched binding of DRM arose in C. elegans as a consequence of germline X chromosome silencing and the evolutionary redistribution of germline-expressed and essential target genes to autosomes. Sex chromosome gene regulation may thus have profound evolutionary effects on genome organization and transcriptional regulatory networks.

    DOI

  • Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex.

    Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA

    PLoS genetics   7 ( 5 ) e1002074  2011.05  [Refereed]

    DOI PubMed

  • Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like

    Saori Nagayoshi, Eriko Hayashi, Gembu Abe, Naoki Osato, Kazuhide Asakawa, Akihiro Urasaki, Kazuki Horikawa, Kazuho Ikeo, Hiroyuki Takeda, Koichi Kawakami

    DEVELOPMENT   135 ( 1 ) 159 - 169  2008.01  [Refereed]

    　View Summary

    Gene trap and enhancer trap methods using transposon or retrovirus have been recently described in zebrafish. However, insertional mutants using these methods have not been reported. We report here development of an enhancer trap method by using the Tol2 transposable element and identification and characterization of insertional mutants. We created 73 fish lines that carried single copy insertions of an enhancer trap construct, which contained the zebrafish hsp70 promoter and the GFP gene, in their genome and expressed GFP in specific cells, tissues and organs, indicating that the hsp70 promoter is highly capable of responding to chromosomal enhancers. First, we analyzed genomic DNA surrounding these insertions. Fifty-one of them were mapped onto the current version of the genomic sequence and 43% (22/51) were located within transcribed regions, either exons or introns. Then, we crossed heterozygous fish carrying the same insertions and identified two insertions that caused recessive mutant phenotypes. One disrupted the tcf7 gene, which encodes a transcription factor of the Tcf/Lef family mediating Wnt signaling, and caused shorter and wavy median fin folds and pectoral fins. We knocked down Lef1, another member of the Tcf/Lef family also expressed in the fin bud, in the tcf7 mutant, and revealed functional redundancy of these factors and their essential role in establishment of the apical ectodermal ridge (AER). The other disrupted the synembryn-like gene (synbl), a homolog of the C. elegans synembryn gene, and caused embryonic lethality and small pigment spots. The pigment phenotype was rescued by application of forskolin, an activator of adenylyl cyclase, suggesting that the synbl gene activates the G(alpha s) pathway leading to activation of adenylyl cyclase. We thus demonstrated that the transposon-mediated enhancer trap approach can indeed create insertional mutations in developmental genes. Our present study provides a basis for the development of efficient transposon-mediated insertional mutagenesis in a vertebrate.

    DOI PubMed

  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

    Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, Jun-Ichi Takeda, Takayuki Taniya, Ryuichi Sakate, Shingo Kikugawa, Makoto Shimada, Motohiko Tanino, Kanako O. Koyanagi, Roberto A. Barrero, Craig Gough, Hong-Woo Chun, Takuya Habara, Hideki Hanaoka, Yosuke Hayakawa, Phillip B. Hilton, Yayoi Kaneko, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Akihiro Matsuya, Naoki Nagata, Kensaku Nishikata, Akiko Ogura Noda, Shin Nurimoto, Naomi Saichi, Hiroaki Sakai, Ryoko Sanbonmatsu, Rie Shiba, Mami Suzuki, Kazuhiko Takabayashi, Aiko Takahashi, Takuro Tamura, Masayuki Tanaka, Susumu Tanaka, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Toshihisa Okido, Jun Mashima, Aki Hashizume, Lihua Jin, Kyung-Bum Lee, Yi-Chueh Lin, Asami Nozaki, Katsunaga Sakai, Masahito Tada, Satoru Miyazaki, Takashi Makino, Hajime Ohyanagi, Naoki Osato, Nobuhiko Tanaka, Yoshiyuki Suzuki, Kazuho Ikeo, Naruya Saitou, Hideaki Sugawara, Claire O'Donovan, Tamara Kulikova, Eleanor Whitfield, Brian Halligan, Mary Shimoyama, Simon Twigger, Kei Yura, Kouichi Kimura, Tomohiro Yasuda, Tetsuo Nishikawa, Yutaka Akiyama, Chie Motono, Yuri Mukai, Hideki Nagasaki, Makiko Suwa, Paul Horton, Reiko Kikuno, Osamu Ohara, Doron Lancet, Eric Eveno, Esther Graudens, Sandrine Imbeaud, Marie Anne Debily, Yoshihide Hayashizaki, Clara Amid, Michael Han, Andreas Osanger, Toshinori Endo, Michael A. Thomas, Mika Hirakawa, Wojciech Makalowski, Mitsuteru Nakao, Nam-Soon Kim, Hyang-Sook Yoo, Sandro J. De Souza, Maria de Fatima Bonaldo, Yoshihito Niimura, Vladimir Kuryshev, Ingo Schupp, Stefan Wiemann, Matthew Bellgard, Masafumi Shionyu, Libin Jia, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, Qinghua Zhang, Mitiko Go, Shinsei Minoshima, Masafumi Ohtsubo, Kousuke Hanada, Peter Tonellato, Takao Isogai, Ji Zhang, Boris Lenhard, Sangsoo Kim, Zhu Chen, Ursula Hinz, Anne Estreicher, Kenta Nakai, Izabela Makalowska, Winston Hide, Nicola Tiffin, Laurens Wilming, Ranajit Chakraborty, Marcelo Bento Soares, Maria Luisa Chiusano, Yutaka Suzuki, Charles Auffray, Yumi Yamaguchi-Kabata, Takeshi Itoh, Teruyoshi Hishiki, Satoshi Fukuchi, Ken Nishikawa, Sumio Sugano, Nobuo Nomura, Yoshio Tateno, Tadashi Imanishi, Takashi Gojobori

    NUCLEIC ACIDS RESEARCH   36 ( Database issue ) D793 - D799  2008.01  [Refereed]

    　View Summary

    Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, proteinprotein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

    DOI PubMed

  • The evolutionary emergence of cell type-specific genes inferred from the gene expression analysis of Hydra

    Jung Shan Hwang, Hajime Ohyanagi, Shiho Hayakawa, Naoki Osato, Chiemi Nishimiya-Fujisawa, Kazuho Ikeo, Charles N. David, Toshitaka Fujisawa, Takashi Gojobori

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   104 ( 37 ) 14735 - 14740  2007.09  [Refereed]

    　View Summary

    Cell lineages of cnidarians including Hydra represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal kingdom. Hydra contains epithelial cells as well as a multipotent interstitial cell (1-cell) that gives rise to nematocytes, nerve cells, gland cells, and germ-line cells. We used cDNA microarrays to identify cell type-specific genes by comparing gene expression in normal Hydra with animals lacking the 1-cell lineage, so-called epithelial Hydra. We then performed in situ hybridization to localize expression to specific cell types. Eighty-six genes were shown to be expressed in specific cell types of the 1-cell lineage. An additional 29 genes were expressed in epithelial cells and were down-regulated in epithelial animals lacking 1-cells. Based on the above information, we constructed a database (http://hydra.lab. nig.ac.jp/hydra/), which describes the expression patterns of cell type-specif ic genes in Hydra. Most genes expressed specifically in either 1-cells or epithelial cells have homologues in higher metazoans. By comparison, most nematocyte-specific genes and approximately half of the gland cell- and nerve cell-specif ic genes are unique to the cnidarian lineage. Because nematocytes, gland cells, and nerve cells appeared along with the emergence of cnidarians, this suggests that lineage-specific genes arose in cnidarians in conjunction with the evolution of new cell types required by the cniclarians.

    DOI PubMed

  • Transcriptional interferences in cis natural antisense transcripts of humans and mice

    Naoki Osato, Yoshiyuki Suzuki, Kazuho Ikeo, Takashi Gojobori

    GENETICS   176 ( 2 ) 1299 - 1306  2007.06  [Refereed]

    　View Summary

    For a significant fraction of mRNA-s, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands of DNA at the same genomic locus. The regulatory mechanism of mRNA expression by cis-NATs is unknown, although a few possible explanations have been proposed. To understand this regulatory mechanism, we conducted a large-scale analysis of the currently available data and examined how the overlapping arrangements of cis-NATs affect their expression level. Here, we show that for both human and mouse the expression level of cis-NATs decreases as the length of the overlapping region increases. In particular, the proportions of the highly expressed cis-NATs in all cis-NATs examined were similar to 36 and 47% for human and mouse, respectively, when the overlapping region was &lt; 200 bp. However, both proportions decreased to virtually zero when the overlapping regions were &gt; 2000 bp in length. Moreover, the distribution of the expression level of cis-NATs changes according to different types of the overlapping pattern of cis-NATs in the genome. These results are consistent with the transcriptional collision model for the regulatory mechanism of gene expression by cis-NATs.

    DOI PubMed

  • Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project

    Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B. Hilton, Baltazar A. Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Antonio Costa De Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T. Hiraki, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue-Ie Hsing, Hiroshi Ikawa, Kazuho Ikeo, Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hiroaki Kawashima, Jitendra P. Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O. Koyanagi, Hiromi Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W. Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O'Donovan, Hajime Ohyanagi, Toshihisa Okido, Satoshi OOta, Naoki Osato, Lance E. Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K. Singh, Brian Smith-White, Jun-Ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Mika Tsugane, Akhilesh K. Tyagi, Apichart Vanavichit, Aihui Wang, Rod A. Wing, Kaori Yamaguchi, Mayu Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Gojobori, Takuji Sasaki

    Genome Research   17 ( 2 ) 175 - 183  2007.02  [Refereed]

    　View Summary

    We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. ©2007 by Cold Spring Harbor Laboratory Press.

    DOI PubMed

  • Development of a Computer-Based Method for a Full-Length cDNA Project and Discovery of Cis Sense-Antisense mRNAs with Full-Length cDNAs

    Naoki Osato

    Doctoral thesis    2007  [Refereed]

  • A genome-wide and nonredundant mouse transcription factor database

    M Kanamori, H Konno, N Osato, J Kawai, Y Hayashizaki, H Suzuki

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   322 ( 3 ) 787 - 793  2004.09  [Refereed]

    　View Summary

    Here we describe the development of a genome-wide and nonredundant mouse transcription factor database and its viewer (http://genome.gsc.riken.jp/TFdb/). We systematically selected transcription factors with DNA-binding properties and their regulators on the basis of their LocusLink and Gene Ontology annotations. We also incorporated into our database information regarding the corresponding available cDNA clones and their structural properties. Because of these features, our database is unique and may provide useful information for systematic genome-wide studies of transcriptional regulation. (C) 2004 Elsevier Inc. All rights reserved.

    DOI PubMed

  • Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR

    H Suzuki, R Okunishi, W Hashizume, S Katayama, N Ninomiya, N Osato, K Sato, M Nakamura, J Iida, M Kanamori, Y Hayashizaki

    FEBS LETTERS   573 ( 1-3 ) 214 - 218  2004.08  [Refereed]

    　View Summary

    We established a medium-scale real-time RT-PCR system focusing on transcription factors and applied it to their expression profiles in the adult mouse 11 brain regions (http:// genome.gsc.riken.jp/qRT-PCR/). Almost 90% of the examined genes showed significant expression in at least one region. We successfully extracted 179 region-specific genes by clustering analysis. Interestingly, the transcription factors involved in the development of the pituitary were still expressed in the adult pituitary, suggesting that they also play important roles in maintenance of the pituitary. These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

    DOI PubMed

  • Antisense transcripts with rice full-length cDNAs

    N Osato, H Yamada, K Satoh, H Ooka, M Yamamoto, K Suzuki, J Kawai, P Carninci, Y Ohtomo, K Murakami, K Matsubara, S Kikuchi, Y Hayashizaki

    GENOME BIOLOGY   5 ( 1 )  2004  [Refereed]

    　View Summary

    Background: Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs.
    Results: We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86%) had coding potential.
    Conclusions: The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts.

  • Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana

    H Ooka, K Satoh, K Doi, T Nagata, Y Otomo, K Murakami, K Matsubara, N Osato, J Kawai, P Carninci, Y Hayashizaki, K Suzuki, K Kojima, Y Takahara, K Yamamoto, S Kikuchi

    DNA RESEARCH   10 ( 6 ) 239 - 247  2003.12  [Refereed]

    　View Summary

    The NAC domain was originally characterized from consensus sequences from petunia NAM and from Arabidopsis ATAF1, ATAF2, and CUC2. Genes containing the NAC domain (NAC family genes) are plant-specific transcriptional regulators and are expressed in various developmental stages and tissues. We performed a comprehensive analysis of NAC family genes in Oryza sativa (a monocot) and Arabidopsis thaliana (a dicot). We found 75 predicted NAC proteins in full-length cDNA data sets of O. sativa (28,469 clones) and 105 in putative genes (28,581 sequences) from the A. thaliana genome. NAC domains from both predicted and known NAC family proteins were classified into two groups and 18 subgroups by sequence similarity. There were a few differences in amino acid sequences in the NAC domains between O. saliva and A. thaliana. In addition, we found 13 common sequence motifs from transcriptional activation regions in the C-terminal regions of predicted NAC proteins. These motifs probably diverged having correlations with NAC domain structures. We discuss the relationship between the structure and function of the NAC family proteins in light of our results and the published data. Our results will aid further functional analysis of NAC family genes.

    DOI PubMed

  • Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice

    S Kikuchi, K Satoh, T Nagata, N Kawagashira, K Doi, N Kishimoto, J Yazaki, M Ishikawa, H Yamada, H Ooka, Hotta, I, K Kojima, T Namiki, E Ohneda, W Yahagi, K Suzuki, CJ Li, K Ohtsuki, T Shishiki, Y Otomo, K Murakami, Y Iida, S Sugano, T Fujimura, Y Suzuki, Y Tsunoda, T Kurosaki, T Kodama, H Masuda, M Kobayashi, QH Xie, M Lu, R Narikawa, A Sugiyama, K Mizuno, S Yokomizo, J Niikura, R Ikeda, J Ishibiki, M Kawamata, A Yoshimura, J Miura, T Kusumegi, M Oka, R Ryu, M Ueda, K Matsubara, J Kawai, P Carninci, J Adachi, K Aizawa, T Arakawa, S Fukuda, A Hara, W Hashizume, N Hayatsu, K Imotani, Y Ishii, M Itoh, Kagawa, I, S Kondo, H Konno, A Miyazaki, N Osato, Y Ota, R Saito, D Sasaki, K Sato, K Shibata, A Shinagawa, T Shiraki, M Yoshino, Y Hayashizaki, A Yasunishi

    SCIENCE   301 ( 5631 ) 376 - 379  2003.07  [Refereed]

    　View Summary

    We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.

    DOI PubMed

  • Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia

    P Carninci, K Waki, T Shiraki, H Konno, K Shibata, M Itoh, K Aizawa, T Arakawa, Y Ishii, D Sasaki, H Bono, S Kondo, Y Sugahara, R Saito, N Osato, S Fukuda, K Sato, A Watahiki, T Hirozane-Kishikawa, M Nakamura, Y Shibata, A Yasunishi, N Kikuchi, A Yoshiki, M Kusakabe, S Gustincich, K Beisel, W Pavan, Aidinis, V, A Nakagawara, WA Held, H Iwata, T Kono, H Nakauchi, P Lyons, C Wells, DA Hume, M Fagiolini, TK Hensch, M Brinkmeier, S Camper, J Hirota, P Mombaerts, M Muramatsu, Y Okazaki, J Kawai, Y Hayashizaki

    GENOME RESEARCH   13 ( 6B ) 1273 - 1289  2003.06  [Refereed]

    　View Summary

    We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to &gt;12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large. numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, S'-end clusters identify regions that are potential promoters for 8637 known genes and S'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.

    DOI PubMed

  • Antisense transcripts with FANTOM2 clone set and their implications for gene regulation

    H Kiyosawa, Yamanaka, I, N Osato, S Kondo, Y Hayashizaki

    GENOME RESEARCH   13 ( 6B ) 1324 - 1334  2003.06  [Refereed]

    　View Summary

    We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sense-antisense transcript and nonantisense bidirectional transcription pairs in mammals. The FANTOM2 cDNA set appears to contain substantially large numbers of noncoding transcripts suitable for antisense transcript analysis. The average proportion of loci encoding sense-antisense transcript and nonantisense bidirectional transcription pairs on autosomes was 15.1 and 5.4%, respectively. Those on the X chromosome were 6.3 and 4.2%, respectively. Sense-antisense transcript pairs, rather than nonantisense bidirectional transcription pairs, may be less prevalent on the X chromosome, possibly due to X chromosome inactivation. Sense and antisense transcripts tended to be isolated from the same libraries, where nonantisense bidirectional transcription pairs were not apparently coregulated. The existence of large numbers of natural antisense transcripts implies that the regulation of gene expression by antisense transcripts is more common that previously recognized. The viewer showing mapping patterns of sense-antisense transcript pairs and nonantisense bidirectional transcription pairs on the genome and other related statistical data is available on our Web site.

    DOI PubMed

  • Antisense transcripts with rice full-length cDNAs.

    Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y

    Genome biology   5 ( 1 ) R5  2003  [Refereed]

    DOI PubMed

  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

    Y Okazaki, M Furuno, T Kasukawa, J Adachi, H Bono, S Kondo, Nikaido, I, N Osato, R Saito, H Suzuki, Yamanaka, I, H Kiyosawa, K Yagi, Y Tomaru, Y Hasegawa, A Nogami, C Schonbach, T Gojobori, R Baldarelli, DP Hill, C Bult, DA Hume, J Quackenbush, LM Schriml, A Kanapin, H Matsuda, S Batalov, KW Beisel, JA Blake, D Bradt, Brusic, V, C Chothia, LE Corbani, S Cousins, E Dalla, TA Dragani, CF Fletcher, A Forrest, KS Frazer, T Gaasterland, M Gariboldi, C Gissi, A Godzik, J Gough, S Grimmond, S Gustincich, N Hirokawa, IJ Jackson, ED Jarvis, A Kanai, H Kawaji, Y Kawasawa, RM Kedzierski, BL King, A Konagaya, Kurochkin, IV, Y Lee, B Lenhard, PA Lyons, DR Maglott, L Maltais, L Marchionni, L McKenzie, H Miki, T Nagashima, K Numata, T Okido, WJ Pavan, G Pertea, G Pesole, N Petrovsky, R Pillai, JU Pontius, D Qi, S Ramachandran, T Ravasi, JC Reed, DJ Reed, J Reid, BZ Ring, M Ringwald, A Sandelin, C Schneider, CAM Semple, M Setou, K Shimada, R Sultana, Y Takenaka, MS Taylor, RD Teasdale, M Tomita, R Verardo, L Wagner, C Wahlestedt, Y Wang, Y Watanabe, C Wells, LG Wilming, A Wynshaw-Boris, M Yanagisawa, Yang, I, L Yang, Z Yuan, M Zavolan, Y Zhu, A Zimmer, P Carninci, N Hayatsu, T Hirozane-Kishikawa, H Konno, M Nakamura, N Sakazume, K Sato, T Shiraki, K Waki, J Kawai, K Aizawa, T Arakawa, S Fukuda, A Hara, W Hashizume, K Imotani, Y Ishii, M Itoh, Kagawa, I, A Miyazaki, K Sakai, D Sasaki, K Shibata, A Shinagawa, A Yasunishi, M Yoshino, R Waterston, ES Lander, J Rogers, E Birney, Y Hayashizaki

    NATURE   420 ( 6915 ) 563 - 573  2002.12  [Refereed]

    　View Summary

    Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 &apos;transcriptional units&apos;, contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

    DOI PubMed

  • A computer-based method of selecting clones for a full-length cDNA project: Simultaneous collection of negligibly redundant and variant cDNAs

    N Osato, M Itoh, H Konno, S Kondo, K Shibata, P Carninci, T Shiraki, A Shinagawa, T Arakawa, S Kikuchi, K Sato, J Kawai, Y Hayashizaki

    GENOME RESEARCH   12 ( 7 ) 1127 - 1134  2002.07  [Refereed]

    　View Summary

    We describe a computer-based method that selects representative clones for full-length sequencing in a full-length cDNA project. Our method classifies end sequences using two kinds of criteria, grouping, and clustering. Grouping places together variant cDNAs, family genes, and cDNAs with sequencing errors. Clustering separates those cDNA clones into distinct Clusters. The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined. Grouping reduced the number of rice cDNA clones for full-length sequencing to 21% and mouse cDNA clones to 25%. Rice full-length sequences selected by grouping showed a 1.07-fold redundancy. Mouse full-length sequences showed a 1.04-fold redundancy, which can be reduced by similar to30% from the selection using our previous method. To estimate the coverage of unique genes, we used FANTOM (Functional Annotation of RIKEN Mouse cDNA Clones) clusters (the RIKEN Genome Exploration Research Group 2001). Grouping covered almost all unique genes (93% of FANTOM clusters), and clustering covered all genes. Therefore, our method is useful for the selection of appropriate representative clones for full-length Sequencing, thereby greatly reducing the cost, labor, and time necessary for this process.

    DOI PubMed

  • Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing

    Shibata, I, P Carninci, K Sato, N Hayatsu, T Shiraki, Y Ishii, T Arakawa, A Hara, N Ohsato, M Izawa, K Aizawa, M Itoh, K Shibata, A Shinagawa, J Kawai, Y Ota, S Kikuchi, N Kishimoto, M Muramatsu, Y Hayashizaki

    BIOTECHNIQUES   31 ( 5 ) 1042 - +  2001.11  [Refereed]

    　View Summary

    We have developed a method to overcome sequencing problems caused by the presence of homopolymer stretches, such as polyA/T in cDNA libraries. PolvA tails are shortened by cleaving before cDNA cloning with type IIS restriction enzymes, such as GsuI, placed next to the oligo-dT used to prime the polyA tails of mRNAs. We constructed four rice Cap-Trapper-selected. full-length normalized cDNA libraries, of which the average residual polyA tail was 4 bases or shorter in most of the clones analyzed. Because of the removal of homopolymeric stretches, libraries prepared with this method can be used for direct sequencing and transcriptional sequencing without the slippage observed for libraries prepared with currently available methods, thus improving sequencing accuracy, operations, and throughput.

    PubMed

  • Clustering of Full-Length cDNA Clones Based on Both End Sequences

    Osato Naoki, Konno Hideki, Itoh Masayoshi, Condo Shinji, Kawai Jun, Shibata Kazuhiro, Shinagawa Akira, Apache Jun, Fukuda Shiro, Ota Yoshimi, Hayashizaki Yoshihide

    Genome Informatics   11   374 - 375  2000  [Refereed]

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Books and Other Publications

  • Topics 実験データ解析と機械学習による転写制御因子の探索、特集 エピトランスクリプトミクス

    大里直樹、浜田道昭

    月刊細胞、ニューサイエンス社  2021.12

  • Topics 実験データ解析による転写制御因子の探索、特集 ゲノムデータを駆使した医学研究

    大里直樹( Part： Sole author)

    月刊細胞、ニューサイエンス社  2021.07

  • Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs

    Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada( Part： Joint author)

    Preprints  2021

  • ゲノムの進化、淘汰、中立 生物の科学 遺伝別冊No.20 進化でどこまでわかるか？

    Giorgio Bernardi 著, 大里直樹, 五條堀孝

    NTS  2007

  • Genome Science of Vertebrate

    Osato N, Kiyosawa H, Kawai J, Hayashizaki Y

    EOLSS (The Encyclopedia of Life Support Systems), UNESCO  2004

  • 分子生物学のためのバイオインフォマティクス入門

    大里直樹( Part： Sole translator, 第9章 エピローグ：DNAを用いたコンピュータ)

    共立出版株式会社  2001

  • 解読されたゲノム情報をどう活かすか 現代化学増刊40号

    近藤伸二, 大里直樹( Part： Joint author, 3. ヒト総遺伝子数)

    東京化学同人  2001

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Awards

  • IPSJ Yamashita SIG Research Award

    2018.08   Information Processing Society of Japan   Characteristic of functional enrichment of putative transcriptional target genes and its application

    Winner： Naoki Osato

  • SIGBIO Excellent Presentation Award

    2018.05   Information Processing Society of Japan, Bioinformatics and Genomics(BIO)   Characteristics of functional enrichement of putative transcriptional target genes and its application

    Winner： Naoki Osato

Research Projects

  • エンハンサーに関わるDNA配列と遺伝子発現に影響する転写因子の網羅的な探索

    住友財団  基礎科学研究助成

    Project Year :

    2021.11
    -
    2022.11
     

  • 深層学習による生物実験データ解析法と研究仮説検証法の開発

    早稲田大学  早大理工総研ーキオクシア若手奨励研究

    Project Year :

    2021
    -
    2022.02
     

    大里直樹

  • 遺伝子転写制御のゲノムワイドな予測法の開発

    大阪大学 情報科学研究科  スタートアッププログラム

    Project Year :

    2020
    -
    2021.03
     

    大里直樹

  • 線虫のゲノムワイドな転写制御ネットワーク解析

    山田科学振興財団  海外長期間派遣援助

    Project Year :

    2009.04
    -
    2010.03
     

    大里直樹

  • 統計モデルによるゲノムワイドな遺伝子転写カスケード解析法の開発

    文部科学省  科学研究費補助金 基盤研究（C）

    大里直樹

Presentations

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発

    大里直樹、浜田道昭

    第44回日本分子生物学会年会 

    Presentation date： 2021.12

    Event date：
    2021.12
    　
    　

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発

    大里直樹, 浜田道昭

    第68回バイオ情報学研究会 

    Presentation date： 2021.11

  • 深層学習を用いた、ヒトのエンハンサー・遺伝子相互作用に影響する転写因子の解析.

    大里直樹, 浜田道昭

    JST CREST 「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」 キックオフシンポジウム「バイオDXの最前線 

    Presentation date： 2021.11

    Event date：
    2021.11
    　
    　

  • 深層学習の予測結果に寄与する因子の大規模な解析に伴うノイズの影響の低減

    大里直樹、浜田道昭

    第24回情報論的学習理論ワークショップ 

    Presentation date： 2021.11

    Event date：
    2021.11
    　
    　

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発

    大里直樹, 浜田道昭

    第67回バイオ情報学研究会 

    Presentation date： 2021.09

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見

    大里直樹, 浜田道昭

    第10回生命医薬情報学連合大会 

    Presentation date： 2021.09

  • Systematic discovery of directional chromatin-associated regulatory motifs affecting human gene transcription

    Naoki Osato

    Intelligent Systems for Molecular Biology (ISMB) 

    Presentation date： 2021.07

  • ヒトのオープンクロマチン領域に存在する転写因子DNA結合配列の網羅的な解析

    大里直樹

    日本遺伝学会第92回大会 

    Presentation date： 2020.09

  • ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析

    大里直樹

    第9回生命医薬情報学連合大会 

    Presentation date： 2020.09

  • Discovery of biased orientations of regulatory motifs affecting transcription of human genes and including known insulators

    Naoki Osato

    Conference on Intelligent Systems for Molecular Biology (ISMB) 2020 

    Presentation date： 2020.07

  • ヒト転写因子の標的遺伝子の特徴とインシュレータ機能に関わるDNA配列の発見

    大里直樹

    遺伝学会春季分科会 

    Presentation date： 2020.03

  • 脂肪細胞におけるSTAT3を介したUCP1発現制御機構の解明

    疋田菜光, 岩瀬麻里, 川原崎聡子, 酒井章子, 坂本智弥, 大里直樹, 瀬尾茂人, 野村亘, 野村亘, 高橋春弥, 松田秀雄, 井上和生, 井上和生, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    日本栄養・食糧学会近畿支部大会および公開シンポジウム講演抄録集 

    Presentation date： 2020

    Event date：
    2020
    　
    　

  • Characteriistic of human putative transcriptional target genes and discovery of biased orientations of DNA motifs affecting transcription of genes.

    Naoki Osato

    Presentation date： 2019.12

  • Characteristic of human putative transcriptional target genes and discovery of biased orientaions of DNA motifs affecting transcription of genes

    Naoki Osato  [Invited]

    Presentation date： 2019.12

  • 脂肪組織におけるglycerol kinaseのUcp1発現制御機構

    岩瀬 麻里, 常盤 颯志, 瀬尾 茂人, 向井 貴子, 高橋 春弥, 野村 亘, Jheng Huei-Fen, 楠堂 達也, 大里 直樹, 松田 秀雄, 井上 和生, 河田 照雄, 後藤 剛

    肥満研究  (一社)日本肥満学会

    Presentation date： 2019.10

    Event date：
    2019.10
    　
    　

  • ヒト転写因子の転写標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析

    大里 直樹

    日本遺伝学会第91回大会 

    Presentation date： 2019.09

  • ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析

    大里 直樹  [Invited]

    第8回生命医薬情報学連合大会年会 

    Presentation date： 2019.09

  • Characteristics of human putative transcriptional target genes and discovery of biased orientation of DNA motifs affecting transcription of genes

    Naoki Osato

    Conference on Intelligent Systems for Molecular Biology (ISMB) 

    Presentation date： 2019.07

  • A method for inferring gene regulatory networks based on pseudo time-series gene expression profiles from single-cell RNA-seq data

    Kaito Uemura, Naoki Osato, Hironori Shigeta, Shigeto Seno, Hideo Matsuda

    Conference on Intelligent Systems for Molecular Biology (ISMB) 

    Presentation date： 2019.07

  • 白色脂肪組織の褐色化に対するglycerol kinaseの役割

    岩瀬麻里, 常盤颯志, 瀬尾茂人, 向井貴子, 高橋春弥, 野村亘, 野村亘, JHENG Huei‐Fen, 荒武, 楠堂達也, 大里直樹, 松田秀雄, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    日本栄養・食糧学会大会講演要旨集 

    Presentation date： 2019.04

    Event date：
    2019.04
    　
    　

  • Single-cell transcriptome analysis for elucidating cell dynamics

    Naoki Osato, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Hideo Matsuda

    12th international workshop on approaches to single cell analysis 

    Presentation date： 2019.03

  • ヒト転写因子の標的遺伝子の特徴とエンハンサー・遺伝子相互作用に関わる転写因子解析

    大里 直樹

    遺伝学会春季分科会 

    Presentation date： 2019.03

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見

    大里直樹

    第41回日本分子生物学会年会 

    Presentation date： 2018.11

  • IL‐1βが白色脂肪組織におけるUCP1発現誘導に及ぼす影響の検討

    新谷真和, 吉竹里依子, 岩瀬麻里, 高橋春弥, 野村亘, JHENG Huie‐Fun, 荒武, 大里直樹, 瀬尾茂人, 松田秀雄, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    肥満研究 

    Presentation date： 2018.09

    Event date：
    2018.09
    　
    　

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見

    大里直樹

    日本遺伝学会第90回大会 

    Presentation date： 2018.09

  • ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見

    大里直樹

    第7回生命医薬情報学連合大会(IIBMP) 

    Presentation date： 2018.09

  • Ucp1発現を制御するnon‐coding RNAの探索と機能解析

    岩瀬麻里, 酒井章子, 瀬尾茂人, TONY Kuo, 高橋春弥, 野村亘, 野村亘, JHENG Huie‐Fun, 荒武, PAUL Horton, 大里直樹, 松田秀雄, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    日本農芸化学会大会講演要旨集(Web) 

    Presentation date： 2018.03

    Event date：
    2018.03
    　
    　

  • DPP‐4阻害剤テネリグリプチンが脂肪組織のUCP‐1発現に与える影響

    澤崎穂菜美, 武田健一郎, 高橋春弥, 野村亘, 野村亘, JHENG Huei‐fen, 荒武, 高橋信之, 高橋信之, 大里直樹, 瀬尾茂人, 松田秀雄, 河田照雄, 後藤剛

    日本農芸化学会大会講演要旨集(Web) 

    Presentation date： 2018.03

    Event date：
    2018.03
    　
    　

  • 褐色脂肪細胞機能におけるglycerol kinaseの役割

    岩瀬麻里, 常盤颯志, 高橋春弥, 野村亘, 野村亘, JHENG Huei-Fun, 荒武, 大里直樹, 瀬尾茂人, 松田秀雄, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    日本食品科学工学会関西支部大会市民フォーラム講演要旨集 

    Presentation date： 2018

    Event date：
    2018
    　
    　

  • Chromatin accessibility dynamics reveal decrease of DNA motif sequences of transcription factors during macrophage aging

    Naoki Osato

    International Meeting on RECQ Helicases and Related Diseases 

    Presentation date： 2018

  • Discovery of biased orientation of DNA motif sequences affecting human gene expression for prediction of enhancer-promoter interactions

    Naoki Osato

    Human Genome Meeting 2018 

    Presentation date： 2018

  • 発現制御に関するmiRNAの探索及び機能解析

    酒井章子, 大久保麻里, 高橋春弥, 野村亘, 野村亘, JHENG Huie‐Fen, 荒武, 瀬尾茂人, 大里直樹, 松田秀雄, 河田照雄, 河田照雄, 後藤剛, 後藤剛

    日本栄養・食糧学会近畿支部大会および公開シンポジウム講演抄録集 

    Presentation date： 2017.11

    Event date：
    2017.11
    　
    　

  • UCP1発現制御に関するmiRNAの探索及び機能解析

    酒井章子

    第56回日本栄養・食糧学会年会 

    Presentation date： 2017

  • DPP-4阻害剤テネリグリプチンが脂肪組織のUCP-1発現に与える影響

    澤崎穂菜美

    農芸化学学会年会 

    Presentation date： 2017

  • Ucp1発現を制御するnon-coding RNAの探索と機能解析

    岩瀬麻里

    農芸化学学会年会 

    Presentation date： 2017

  • Characteristic of functional enrichment of putative transcriptional target genes and its application

    Naoki Osato

    Presentation date： 2017

  • ヒト転写標的遺伝子の機能エンリッチメントの特徴とクロマチン相互作用に関わるタンパク質のDNA結合配列解析への応用

    大里直樹  [Invited]

    第40回日本分子生物学会年会 

    Presentation date： 2017

  • Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes (2)

    Naoki Osato

    The 12th International Workshop on Advanced Genomics 

    Presentation date： 2017

  • Characteristics of functional enrichment of human putative transcriptional target genes

    Naoki Osato

    Presentation date： 2017

  • Methylation diversity among human vascular endothelial cells

    Genta Nagae, Youichiro Wada, Ryuichiro Nakato, Takayoshi Umeda, Yuki Katou, Shuichi Tsutsumi, Naoki Osato, Yasuharu Kanki, Mika Kobayashi, Akashi Izumi-Taguchi, Yutaka Saito, Toutai Mitsuyma, Hiroshi Kimura, Katsuhiko Shirahige, Hiroyuki Aburatani

    The 12 th International Workshop on Advanced Genomics  (Japan) 

    Presentation date： 2017

  • １細胞RNA-seqの特性を考慮した遺伝子発現差解析手法の検討

    大里直樹

    NGS現場の会第五回研究会要旨 

    Presentation date： 2017

  • Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

    Naoki Osato

    International Conference on Bioinformatics (InCoB)  (Shenzhen Convention & Exhibition Center, Shenzhen, China) 

    Presentation date： 2017

  • Prediction of transcriptional target genes and its association with their functional enrichments

    Naoki Osato

    Presentation date： 2016

  • Genome-wide analysis of human putative transcriptional target genes reveals significant functional enrichments

    Naoki Osato  [Invited]

    Presentation date： 2016

  • 遺伝子転写カスケード解明のための統合解析(2)

    大里直樹

    生命動態システム科学四拠点,CREST,PRESTO,QBIC合同シンポジウム「生命動態の分子メカニズムと数理」 

    Presentation date： 2016

  • A ROLE OF THE TRANSCRIPTION FACTOR IRF8 IN BASOPHIL AND MAST CELL DEVELOPMENT

    Haruka Sasaki, Daisuke Kurotaki, Naoki Osato, Hideaki Sato, Izumi Sasaki, Shin-ichi Koizumi, Hongsheng Wang, Chika Kaneda, Akira Nishiyama, Tsuneyasu Kaisho, Hiroyuki Aburatani, Herbert C. Morse, Keiko Ozato, Tomohiko Tamura

    EXPERIMENTAL HEMATOLOGY  ELSEVIER SCIENCE INC

    Presentation date： 2015.09

    Event date：
    2015.09
    　
    　

  • Functional enrichment analysis of human transcriptional target genes and its application to their prediction

    Naoki Osato

    IHEC (International Human Epigenome Consortium) Annual Meeting  (Japan) 

    Presentation date： 2015

  • Integrative analysis improves the prediction of key transcription factors and transcriptional activators for cell differentiation

    Naoki Osato

    The 11th International Workshop on Advanced Genomics  (Japan) 

    Presentation date： 2015

  • 遺伝子転写カスケード解明のための統合解析

    大里直樹

    数学協働プログラム「生命ダイナミクスの数理とその応用：理論からのさらなる深化」 

    Presentation date： 2015

  • Genome-wide analysis of human transcriptional target genes reveals significant functional enrichments(2)

    Naoki Osato

    生命医薬情報学連合大会2015年大会要旨 

    Presentation date： 2015

  • ヒト転写標的遺伝子の機能の偏りと転写標的遺伝子予測への応用

    大里直樹

    第87日本遺伝学会年会要旨 

    Presentation date： 2015

  • Genome-wide analysis of human transcriptional target genes reveals significant functional enrichments, improving the prediction of transcriptional cascades

    Naoki Osato

    第15回東京大学生命科学シンポジウム要旨 

    Presentation date： 2015

  • Genome-wide analysis of human transcriptional target genes reveals significant functional enrichments

    Naoki Osato  [Invited]

    Annual Conference of Biochemistry and Molecular Biology  (神戸国際会議場) 

    Presentation date： 2015

  • ヒト転写制御カスケード解明のための統合解析法の開発

    大里直樹  [Invited]

    生命医科学域セミナー  (筑波大学) 

    Presentation date： 2015

  • 遺伝子転写制御のバイオインフォマティクス

    大里直樹  [Invited]

    数理科学と分子生物学を融合する研究・教育のアウトリーチについての研究会  (東京大学・玉原国際セミナーハウス) 

    Presentation date： 2015

  • Human transcriptional target genes include significant functional enrichments

    Naoki Osato

    JSBi2014・第3回生命医薬情報学連合大会要旨 

    Presentation date： 2014

  • The Transcription Factor IRF8 is a Key Transcription Factor for Basophil Development

    Daisuke Kurotaki, Haruka Sasaki, Naoki Osato, Izumi Sasaki, Chika Kaneda, Hideaki Sato, Akira Nishiyama, Tsuneyasu Kaisho, Hiroyuki Aburatani, Herbert C. Morse, Keiko Ozato, Tomohiko Tamura

    BLOOD  AMER SOC HEMATOLOGY

    Presentation date： 2013.11

    Event date：
    2013.11
    　
    　

  • The IRF8-KLF4 transcription factor cascade is essential for the development of monocytes

    Daisuke Kurotaki, Naoki Osato, Akira Nishiyama, Michio Yamamoto, Tatsuma Ban, Hideaki Sato, Jun Nakabayashi, Marina Umehara, Masatoshi Nakazawa, Noriko Miyake, Naomichi Matsumoto, Keiko Ozato, Tomohiko Tamura

    CYTOKINE  ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD

    Presentation date： 2013.09

    Event date：
    2013.09
    　
    　

  • The transcription factor IRF8 is a key transcription factor for basophil development

    Daisuke Kurotaki, Haruka Sasaki, Naoki Osato, Izumi Sasaki, Chika Kaneda, Hideaki Sato, Akira Nishiyama, Tsuneyasu Kaisho, Hiroyuki Aburatani, Herbert C. Morse III, Keiko Ozato, Tomohiko Tamura

    55th ASH Annual Meeting and Exposition  (USA) 

    Presentation date： 2013

  • Functional prediction of transcriptional regulations using epigenetic signatures

    Naoki Osato, Hiroyuki Aburatani

    Cold Spring Harbor Laboratory meeting, Systems Biology: Networks  (USA) 

    Presentation date： 2013

  • Comparative epigenomic analysis of human vascular endothelial cells

    Naoki Osato, Hiroshi Kimura, Katsuhiko Shirahige, Hiroyuki Aburatani, Youichiro Wada

    第36回日本分子生物学会年会要旨 

    Presentation date： 2013

  • The transcription factor IRF8 is required for basophil development

    Haruka Sasaki, Daisuke Kurotaki, Naoki Osato, Izumi Sasaki, Kaneda Chika, Hideaki Sato, Akira Nishiyama, Tsuneyasu Kaisho, Hiroyuki Aburatani, Herbert C. Morse III, Keiko Ozato, Tomohiko Tamura

    第42回日本免疫学会学術集会要旨 

    Presentation date： 2013

  • 転写制御解析のためのバイオインフォマティクス

    大里直樹  [Invited]

    バイオインフォマティクス研究会  (横浜市立大学) 

    Presentation date： 2013

  • Epigenomic analysis from human primary cultivated vascular cells

    Youichiro Wada, Yasuharu Kanki, Naoki Osato, Hiroyuki Aburatani, Katsuhiko Shirahige

    IHEC (International Human Epigenome Consortium) 2012 Seoul Meeting  (Korea) 

    Presentation date： 2012

  • Genome-wide analyses revealed the IRF8-KLF4 transcription factor cascade during monocyte differentiation

    Daisuke Kurotaki, Naoki Osato, Akira Nishiyama, Michio Yamamoto, Hideaki Sato, Jun Nakabayashi, Tatsuma Ban, Keiko Ozato, Tomohiko Tamura

    第41回日本免疫学会学術集会要旨 

    Presentation date： 2012

  • 線虫のゲノムワイドな転写制御ネットワーク解析

    大里直樹  [Invited]

    公益財団法人山田科学振興財団2012年度長期間派遣者研究交歓会  (薬業年金会館) 

    Presentation date： 2012

  • IRF8 physically interacts with C/EBPa to inhibit the generation of granulocyte-macrophage progenitors and neutrophils

    Tomohiko Tamura, Michio Yamamoto, Naoki Osato, Daisuke Kurotaki, Kazuhiro Uno, Masatoshi Nakazawa, Akira Nishiyama, Keiko Ozato

    第34回日本分子生物学会年会要旨 

    Presentation date： 2011

  • Genome-wide analyses of transcriptional regulatory networks in immune cells. Towards Comprehensive Understanding of Immune Dynamism

    Naoki Osato, Nakai Kenta

    Towards Comprehensive Understanding of Immune Dynamism (TCUID 2011) 

    Presentation date： 2011

  • 転写制御解析のバイオインフォマティクス

    大里直樹  [Invited]

    バイオインフォマティクスへの招待  (お茶の水女子大学) 

    Presentation date： 2011

  • DNA binding activity of C. elegans LIN-54 is essential for DRM complex in transcriptional repression and development

    Tomoko M Tabuchi, Bart Deplancke, Naoki Osato, Lihua J Zhu, M Inmaculada Barrasa, Melissa M Harrison, H Robert Horvitz, Kirsten A Hagstrom, Albertha JM Walhout

    EMBO Conference Series. C. elegans: Development and Gene Expression  (Germany) 

    Presentation date： 2010

  • 脊椎動物ゲノムのタンパク質非コード領域からのDNAモチーフ配列の探索(3)

    大里直樹, Martin C. Frith

    平成20年度第8回産総研・産技連LS-BT合同研究発表会要旨 

    Presentation date： 2009

  • Human short DNA motifs overrepresented in conserved non-protein-coding sequences

    Naoki Osato  [Invited]

    JST BIRD meeting  (東京大学柏キャンパス) 

    Presentation date： 2009

  • Overrepresented DNA motifs in highly conserved non-protein-coding regions of vertebrate genomes(5)

    Naoki Osato, Martin C. Frith

    The 2nd Taiwan-Japan young researchers conference on computational and systems biology  (Japan) 

    Presentation date： 2008

  • Overrepresented DNA motifs in highly conserved non-protein-coding regions of vertebrate genomes(4)

    Naoki Osato, Martin C. Frith

    The eighth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics  (United Kingdom) 

    Presentation date： 2008

  • Overrepresented DNA motifs in highly conserved non-protein-coding regions of vertebrate genomes(3)

    Naoki Osato, Martin C. Frith

    CBRC symposium 

    Presentation date： 2008

  • Overrepresented DNA motifs in highly conserved non-protein-coding regions of vertebrate genomes(2)

    Naoki Osato, Martin C. Frith

    The 16th CDB meeting on Cis sequence regulation and its evolution 

    Presentation date： 2008

  • 脊椎動物ゲノムのタンパク質非コード領域からのDNAモチーフ配列の探索(2)

    大里直樹, Martin C. Frith

    第80回日本遺伝学会年会要旨 

    Presentation date： 2008

  • 脊椎動物ゲノムのタンパク質非コード領域からのDNAモチーフ配列の探索

    大里直樹, Martin C. Frith

    日本進化学会2008年大会要旨 

    Presentation date： 2008

  • Overrepresented DNA motifs in highly conserved non-protein-coding regions of vertebrate genomes

    Naoki Osato  [Invited]

    JST BIRD meeting  (国立情報学研究所・国際高等セミナーハウス) 

    Presentation date： 2008

  • Searches for human DNA motif sequences through comparative genome analyses of vertebrate genomes

    Naoki Osato  [Invited]

    JST BIRD meeting  (東京大学・ヒトゲノム解析センター) 

    Presentation date： 2008

  • アンチセンスmRNAとDNAモチーフ配列のゲノム配列からの探索

    大里直樹  [Invited]

    国立遺伝学研究所研究会「集団ゲノミクスを考える：ゲノム非タンパク質コード領域の進化」  (国立遺伝学研究所) 

    Presentation date： 2008

  • Identification and characterization of human overlapping transcripts that affect their expression

    Naoki Osato, Takashi Gojobori

    GENES & GENETIC SYSTEMS  GENETICS SOC JAPAN

    Presentation date： 2007.12

    Event date：
    2007.12
    　
    　

  • Expression of human cis natural antisense transcripts affected by their overlapping arrangements in the genome

    Naoki Osato, Yoshiyuki Suzuki, Kazuho Ikeo, Takashi Gojobori

    International Mammalian Genome Conference  (Japan) 

    Presentation date： 2007

  • ヒト及びマウスのOverlapping transcriptsの発現制御における役割

    大里 直樹, 鈴木 善幸, 池尾一穂, 五條堀孝

    CBRC シンポジウム 

    Presentation date： 2007

  • Transcriptional interferences in cis natural antisense transcripts of humans and mice

    Naoki Osato, Yoshiyuki Suzuki, Kazuho Ikeo, Takashi Gojobori

    Annual Conference of the Japanese Society for Bioinformatics 

    Presentation date： 2007

  • 遺伝子発現に影響を及ぼすヒトOverlapping transcriptsの探索

    大里直樹, 五條堀孝

    第79回日本遺伝学会年会要旨 

    Presentation date： 2007

  • 完全長cDNA配列を用いたCis sense-antisense mRNAの探索とその発現解析

    大里直樹  [Invited]

    産業技術総合研究所研究紹介セミナー  (産業技術総合研究所) 

    Presentation date： 2007

  • ヒトとマウスの比較解析から見たCis sense-antisense mRNAsの発現制御機構とその進化的描像

    大里直樹, 鈴木善幸, 池尾一穂, 五條堀孝

    日本進化学会2006年大会要旨 

    Presentation date： 2006

  • Possible regulatory roles of human and mouse overlapping transcripts in gene expression

    Naoki Osato, Ikeo Kazuho, Takashi Gojobori

    Evolutionary Genomics  (Italy) 

    Presentation date： 2005

  • ヒトOverlapping transcriptsの発現制御における役割

    大里直樹, 池尾一穂, 五條堀孝

    第28回日本分子生物学会年会要旨 

    Presentation date： 2005

  • ヒト及びマウスのOverlapping transcriptsの発現制御における役割(2)

    大里直樹, 池尾一穂, 五條堀孝

    第77回日本遺伝学会年会要旨 

    Presentation date： 2005

  • ヒト及びマウスのOverlapping transcriptsの発現制御における役割

    大里直樹, 池尾一穂, 五條堀孝  [Invited]

    新しいRNA/RNPを見つける会in鶴岡  (慶應義塾大学・先端生命科学研究所) 

    Presentation date： 2005

  • アンチセンスmRNA候補遺伝子の生物種間の比較解析

    大里直樹, 池尾一穂, 五條堀孝

    第27回日本分子生物学会年会要旨 

    Presentation date： 2004

  • 中規模リアルタイムRT-PCRシステムによる転写制御因子群の発現プロファイリング

    奥西理絵, 鈴木治和, 橋詰航, 片山慎太郎, 二宮紀子, 大里直樹, 佐藤健二郎, 中村真理, 飯田樹里, 金森睦, 林崎良英

    第27回日本分子生物学会年会要旨 

    Presentation date： 2004

  • イネ完全長 cDNA 情報とシロイヌナズナの予測遺伝子情報を用いた転写因子ファミリーの構造解析

    大岡久子, 佐藤浩二, 永田俊文, 大友泰裕, 松原謙一, 村上和雄, 大里直樹, 河合純, カルニンチピエロ, 林崎良英, 鈴木宏史, 小島恵一, 高原美規, 菊池尚志, 山元皓二

    第215回日本作物学会年会要旨 

    Presentation date： 2003

  • イネ(Oryza sativa)完全長cDNAデータ解析－Arabidopsisとイネでの転写因子の比較解析－

    佐藤浩二, 大岡久子, 山田仁美, 田崎公久, 李貞淑, 鈴木宏史, 大里直樹, 大友泰裕, 村上和雄, 松原謙一, 河合純, Carninci P, 林崎良英, 菊池尚志

    第26回日本分子生物学会年会要旨 

    Presentation date： 2003

  • イネ完全長cDNAデータを用いたNACファミリーの比較解析

    大岡久子, 佐藤浩二, 永田俊文, 大友泰裕, 松原謙一, 村上和雄, 大里直樹, 河合純, カルニンチ ピエロ, 林崎良英, 鈴木宏史, 小島恵一, 高原美規, 菊地尚志, 山元皓二

    第103回日本育種学会年会要旨 

    Presentation date： 2003

  • イネ完全長 cDNA データを用いた転写因子の比較解析(2)

    大岡久子, 永田俊文, 佐藤浩二, 大友泰裕, 松原謙一, 村上和雄, 大里直樹, 河合純, カルニンチピエロ, 林崎良英, 鈴木宏史, 小島恵一, 高原美規, 山元晧二, 菊池尚志

    第１０２回日本育種学会要旨 

    Presentation date： 2002

  • イネの遺伝子と 3'-UTR の多様性との関係

    佐藤浩二, 小島恵一, 大根田英祐, 矢作渡, 鈴木宏史, 大里直樹, 河合純, カルニンチピエロ, 林崎良英, 大友泰裕, 村上和雄, 松原謙一, 山下智也, 東憲児, 鹿島剛輝, 鷲尾尊規, 冨田勝, 菊池尚志

    第10２回日本育種学会要旨 

    Presentation date： 2002

  • イネの完全長 cDNA における 5'と 3'領域の多型

    佐藤浩二, 小島恵一, 大根田英祐, 矢作渡, 鈴木宏史, 並木高洋, 大里直樹, 河合純, カルニンチピエロ, 林崎良英, 大友泰裕, 村上和雄, 松原謙一, 山下智也, 東憲児, 鹿島剛輝, 鷲尾尊規, 冨田勝, 菊池尚志

    第101回日本育種学会要旨 

    Presentation date： 2002

  • Detection and analysis of transcription factors in mouse full-length cDNAs

    Naoki Osato, Yasuhiro Tomaru, Masanori Suzuki, Jun Kawai, Yoshihide Hayashizaki

    The second Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics  (United Kingdom) 

    Presentation date： 2002

  • Natural Antisense Transcripts in Mice

    清澤秀孔, 山中到, 大里直樹, 林崎良英, 阿部訓也

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • マウスmRNA配列からの転写因子の同定と解析

    大里直樹, 外丸泰浩, 鈴木正則, 河合純, 林崎良英

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • 理研マウス完全長cDNAの全長シーケンス

    荒川貴博, 河合純, カルニンチ ピエロ, 早津徳人, 白木利幸, 岸川(広實)朋子, 伊藤昌可, 石井善幸, 安西亜矢子, 柴田一浩, 相澤克則, 佐々木大輔, 原亜矢子, 香川育子, 福田史郎, 芋谷弘一, 宮崎愛, 橋詰航, 今野英明, 足立淳, 近藤伸二, 大里直樹, 品川朗, 村松正實, 鈴木治和, 岡崎康司, 林崎良英

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • イネ完全長cDNAプロジェクト－全長シーケンス決定－

    福田史郎, 河合純, Carninci Piero, 白木利幸, 岸川(広實)朋子, 伊藤昌可, 荒川貴博, 石井善幸, 柴田一浩, 相澤克則, 香川育子, 佐々木大輔, 橋詰航, 芋谷弘一, 宮崎愛, 大里直樹, 今野英明, 足立淳, 近藤伸二, 岸本直己, 佐藤浩二, 菊池尚志, 林崎良英

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • イネ完全長cDNAデータを用いた転写因子の比較解析

    大岡久子, 永田俊文, 佐藤浩二, 大友泰裕, 松原謙一, 村上和雄, 大里直樹, 河合純, カルニンチ ピエロ, 林崎良英

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • イネ (Oryza sativa) mRNAのpolyA siteの多様性

    佐藤浩二, 小島恵一, 大根田英祐, 矢作渡, 鈴木宏史, 大里直樹, 河合純, カルニンチ ピエロ, 林崎良英, 大友泰裕, 村上和雄, 松原謙一, 山下智也, 東憲児, 鹿島剛輝, 鷲尾尊規, 冨田勝, 菊池尚志

    第25回日本分子生物学会年会要旨 

    Presentation date： 2002

  • コンピュータによる転写調節・翻訳調節に関わる因子の同定とその解析

    大里直樹  [Invited]

    第一回バイオインフォマティクスセミナー  (かずさDNA研究所) 

    Presentation date： 2002

  • イネ完全長cDNAにおけるUTR領域での多型解析

    佐藤浩二, 小島恵一, 大根田英祐, 矢作渡, 並木高洋, 大里直樹, 河合純, カルニンチ ピエロ, 林崎良英, 大友泰裕, 村上和雄, 松原謙一, 山下智也, 鷲尾尊規, 冨田勝, 菊池尚志

    第24回日本分子生物学会年会要旨 

    Presentation date： 2001

  • イネ完全長cDNAプロジェクト－クローン収集とシーケンス決定－

    河合純, カルニンチ ピエロ, 早津徳人, 白木利幸, 広實朋子, 品川朗, 太田由巳, 伊藤昌可, 荒川貴博, 石井善幸, 安西亜矢子, 柴田一浩, 相澤克則, 佐々木大輔, 吉野正康, 原亜矢子, 福田史郎, 香川育子, 大里直樹, 今野英明, 足立淳, 近藤伸二, 斎藤輪太郎, 岸本直己, 佐藤浩二, 菊池尚志, 林崎良英

    第24回日本分子生物学会年会要旨 

    Presentation date： 2001

  • イネ完全長cDNAの全長配列決定候補クローンの選択

    大里直樹, 伊藤昌可, 今野英明, カルニンチ ピエロ, 早津徳人, 白木利幸, 広實朋子, 品川朗, 荒川貴博, 石井善幸, 原亜矢子, 福田史朗, 佐々木大輔, 吉野正康, 安西亜矢子, 柴田一浩, 相澤克則, 近藤伸二, 足立淳, 斎藤輪太郎, 太田由己, 河合純, 林崎良英

    第24回日本分子生物学会年会要旨 

    Presentation date： 2001

  • Clustering of Full-Length cDNA Clones Based on Both End Sequences

    Naoki Osato, Hideaki Konno, Masayoshi Ito, Shinji Kondo, Jun Kawai, Kazuhiro Shibata, Akira Shinagawa, Jun Adachi, Shiro Fukuda, Yoshimi Ota, Yoshihide Hayashizaki

    Genome Informatics  (Japan) 

    Presentation date： 2000

  • イネ完全長cDNAのイネゲノムへのマッピング

    近藤伸二, 太田由巳, 今野英明, 河合純, 伊藤昌可, 柴田一浩, 品川朗, 大里直樹, 齋藤哲哉, 林崎良英

    第23回日本分子生物学会年会要旨 

    Presentation date： 2000

  • イネ完全長cDNAの収集．第23回日本分子生物学会年会要旨

    太田由巳, 河合純, 伊藤昌可, 柴田一浩, 品川朗, カルニンチ ピエロ, 吉野正康, 原亜矢子, 大里直樹, 福田史郎, 早津徳人, 石井善幸, 荒川貴博, 今野英明, 齋藤輪太郎, 相澤克則, 菊池尚志, 大竹祐子, 佐藤浩二, 岸本直己, 林崎良英

    第23回日本分子生物学会年会要旨 

    Presentation date： 2000

  • イネ完全長cDNAの両端配列による分類

    大里直樹, 太田由巳, 福田史郎, 今野英明, 河合純, 伊藤昌可, 柴田一浩, 品川朗, 林崎良英

    第23回日本分子生物学会年会要旨 

    Presentation date： 2000

  • 枯草菌α－アミラーゼにおけるカルシウム結合部位変異と塩素イオン結合部位導入による酵素活性への影響

    大里直樹, 藤本瑞, 門間充, 高瀬研二, 水野洋

    第11回日本蛋白工学会年会要旨 

    Presentation date： 1999

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