O Ohara

Summary

Affiliation: Kazusa DNA Research Institute
Country: Japan

Publications

  1. doi request reprint The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS
    Noriko Okazaki
    Laboratory of Medical Genomics, Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    J Mol Biol 382:257-65. 2008
  2. pmc A Dual Reporter Splicing Assay Using HaloTag-containing Proteins
    Koichi Oshima
    Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Japan Laboratory for Immunogenomics, Research Center for Allergy and Immunology, RIKEN, Yokohama Institute, Yokohama, Japan Department of Pediatrics, Saitama Medical University, Japan
    Curr Chem Genomics 6:27-37. 2012
  3. pmc The FLS (fatty liver Shionogi) mouse reveals local expressions of lipocalin-2, CXCL1 and CXCL9 in the liver with non-alcoholic steatohepatitis
    Toshihisa Semba
    Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1 8 1 Inohana, Chiba 260 8670, Japan
    BMC Gastroenterol 13:120. 2013
  4. ncbi request reprint Cellular and subcellular localization of a newly identified member of the protein 4.1 family, brain 4.1, in the cerebellum of adult and postnatally developing rats
    R Ohara
    Laboratory of DNA Technology, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Japan
    Brain Res Dev Brain Res 117:127-38. 1999
  5. pmc Directional cDNA library construction assisted by the in vitro recombination reaction
    O Ohara
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nucleic Acids Res 29:E22. 2001
  6. ncbi request reprint Characterization of a new beta-spectrin gene which is predominantly expressed in brain
    O Ohara
    Laboratory of DNA Technology, Kazusa DNA Research Institute, Chiba, Japan
    Brain Res Mol Brain Res 57:181-92. 1998
  7. ncbi request reprint Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method
    Osamu Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 9:47-57. 2002
  8. ncbi request reprint Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins
    O Ohara
    Kazusa DNA Research Institute, Chiba, Japan
    DNA Res 4:53-9. 1997
  9. ncbi request reprint [Comprehensive analysis of human large cDNAs which directs the synthesis of large proteins]
    Osamu Ohara
    Tanpakushitsu Kakusan Koso 47:991-6. 2002
  10. doi request reprint From transcriptome analysis to immunogenomics: current status and future direction
    Osamu Ohara
    Department of Human Genome Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    FEBS Lett 583:1662-7. 2009

Collaborators

Detail Information

Publications100

  1. doi request reprint The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS
    Noriko Okazaki
    Laboratory of Medical Genomics, Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    J Mol Biol 382:257-65. 2008
    ..From these findings, we propose a novel model for gene regulation via the SMARCAD1/KIAA1122 protein complex...
  2. pmc A Dual Reporter Splicing Assay Using HaloTag-containing Proteins
    Koichi Oshima
    Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Japan Laboratory for Immunogenomics, Research Center for Allergy and Immunology, RIKEN, Yokohama Institute, Yokohama, Japan Department of Pediatrics, Saitama Medical University, Japan
    Curr Chem Genomics 6:27-37. 2012
    ..We found that the G>C mutation affected CYBB mRNA splicing by changing a delicate balance of splicing efficiencies of introns 4, 5, and 6...
  3. pmc The FLS (fatty liver Shionogi) mouse reveals local expressions of lipocalin-2, CXCL1 and CXCL9 in the liver with non-alcoholic steatohepatitis
    Toshihisa Semba
    Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1 8 1 Inohana, Chiba 260 8670, Japan
    BMC Gastroenterol 13:120. 2013
    ..This study aims to reveal the differences between simple steatosis and NASH...
  4. ncbi request reprint Cellular and subcellular localization of a newly identified member of the protein 4.1 family, brain 4.1, in the cerebellum of adult and postnatally developing rats
    R Ohara
    Laboratory of DNA Technology, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Japan
    Brain Res Dev Brain Res 117:127-38. 1999
    ..These results suggested that brain 4.1 is involved in the formation and maintenance of synapse as a membrane skeletal component at presynaptic terminals in the cerebellum...
  5. pmc Directional cDNA library construction assisted by the in vitro recombination reaction
    O Ohara
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nucleic Acids Res 29:E22. 2001
    ....
  6. ncbi request reprint Characterization of a new beta-spectrin gene which is predominantly expressed in brain
    O Ohara
    Laboratory of DNA Technology, Kazusa DNA Research Institute, Chiba, Japan
    Brain Res Mol Brain Res 57:181-92. 1998
    ....
  7. ncbi request reprint Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method
    Osamu Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 9:47-57. 2002
    ..Taking all these results together, we here conclude that this new method for the construction of size-fractionated cDNA libraries makes it possible to analyze cDNAs efficiently and comprehensively...
  8. ncbi request reprint Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins
    O Ohara
    Kazusa DNA Research Institute, Chiba, Japan
    DNA Res 4:53-9. 1997
    ..The set of libraries constructed here should be very useful for the accumulation of sequence data on large proteins in the human brain...
  9. ncbi request reprint [Comprehensive analysis of human large cDNAs which directs the synthesis of large proteins]
    Osamu Ohara
    Tanpakushitsu Kakusan Koso 47:991-6. 2002
  10. doi request reprint From transcriptome analysis to immunogenomics: current status and future direction
    Osamu Ohara
    Department of Human Genome Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    FEBS Lett 583:1662-7. 2009
    ..This mini-review first describes the historical background of our cDNA project and then provides perspectives on the present and future of immunogenomics based on our experiences...
  11. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 6:337-45. 1999
    ....
  12. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 7:273-81. 2000
    ....
  13. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 8:85-95. 2001
    ....
  14. ncbi request reprint Characterization of cDNA clones in size-fractionated cDNA libraries from human brain
    N Seki
    Kazusa DNA Research Institute, Chiba, Japan
    DNA Res 4:345-9. 1997
    ....
  15. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 7:143-50. 2000
    ....
  16. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 6:63-70. 1999
    ....
  17. ncbi request reprint Identification of high-molecular-weight proteins with multiple EGF-like motifs by motif-trap screening
    M Nakayama
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, 292 0812, Japan
    Genomics 51:27-34. 1998
    ....
  18. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 7:65-73. 2000
    ....
  19. ncbi request reprint Comparison of mRNA and protein levels of four members of the protein 4.1 family: the type II brain 4.1/4.1B/KIAA0987 is the most predominant member of the protein 4.1 family in rat brain
    H Yamakawa
    Laboratory of DNA Technology, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba, Japan
    Gene 248:137-45. 2000
    ..1' and 'type II brain 4.1,' respectively, because these two products were found to be more prominently produced in rat brain than the other two members of the protein 4.1 family, erythroid 4.1 and 4.1G...
  20. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 5:355-64. 1998
    ....
  21. ncbi request reprint Molecular characterization of a new member of the protein 4.1 family (brain 4.1) in rat brain
    H Yamakawa
    Laboratory of DNA Technology, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Brain Res Mol Brain Res 70:197-209. 1999
    ..The existence of multiple forms of the brain 4.1 implies that it has multiple and diverse functions like the erythroid 4.1 gene product...
  22. ncbi request reprint Characterization of a human homolog (BACH1) of the mouse Bach1 gene encoding a BTB-basic leucine zipper transcription factor and its mapping to chromosome 21q22.1
    M Ohira
    Laboratory of Gene Structure, Kazusa DNA Research Institute, Chiba, Japan
    Genomics 47:300-6. 1998
    ..Both the prospective function and the chromosomal location suggest that this gene may be a DS candidate gene, contributing to certain DS phenotypes, and is possibly involved in certain features of monosomy 21...
  23. ncbi request reprint Type II brain 4.1 (4.1B/KIAA0987), a member of the protein 4.1 family, is localized to neuronal paranodes
    R Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Yana 1532 3, Kisarazu 292 0812, Japan
    Brain Res Mol Brain Res 85:41-52. 2000
    ..1G, demonstrated that each of these proteins is distributed in a unique pattern in the cerebellum. Our results are the first to show that type II brain 4.1 is the only member of the protein 4.1 family localized to neuronal paranodes...
  24. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro
    R Kikuno
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 6:197-205. 1999
    ....
  25. ncbi request reprint Characterization of long cDNA clones from human adult spleen
    A Hattori
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 7:357-66. 2000
    ..The results indicated that spleen could be used as an additional source of human long cDNAs to complement the list of human genes...
  26. pmc HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
    R Kikuno
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nucleic Acids Res 28:331-2. 2000
    ..HUGE is available through the WWW at http://www.kazusa.or.jp/huge..
  27. ncbi request reprint A novel method for generating nested deletions using the in vitro bacteriophage T3 DNA packaging system
    Y Kawarabayasi
    Kazusa DNA Research Institute, Chiba, Japan
    DNA Res 1:289-96. 1994
    ..Thus, nested deletion clones that cover the entire region of a approximately 40-kb cosmid insert can be obtained by a single packaging reaction, and its restriction map can be simultaneously obtained...
  28. ncbi request reprint Identification of three novel non-classical cadherin genes through comprehensive analysis of large cDNAs
    D Nakajima
    Department of Human Gene Research, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, 292 0812, Chiba, Japan
    Brain Res Mol Brain Res 94:85-95. 2001
    ....
  29. ncbi request reprint Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro
    K Ishikawa
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 5:169-76. 1998
    ....
  30. ncbi request reprint Identification of novel transcribed sequences on human chromosome 22 by expressed sequence tag mapping
    M Hirosawa
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 8:1-9. 2001
    ..In conclusion, the mapping of ESTs derived from long cDNAs followed by sequencing of the entire cDNAs provided indispensable information for the precise annotation of genes on the genome together with ESTs derived from short cDNAs...
  31. ncbi request reprint Construction of size-fractionated cDNA library assisted by an in vitro recombination reaction
    Osamu Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Chiba, Japan
    Methods Mol Biol 221:59-71. 2003
  32. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 8:319-27. 2001
    ....
  33. ncbi request reprint Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins
    T Nagase
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 8:179-87. 2001
    ....
  34. doi request reprint ORFeome cloning
    Osamu Ohara
    Department of Human Genome Research, Kazusa DNA Research Institute, Chiba, Japan
    Methods Mol Biol 577:3-9. 2009
    ..In this chapter, currently available ORFeome cloning technologies are overviewed and a selection guideline for them is provided...
  35. ncbi request reprint Kazusa mammalian cDNA resources: towards functional characterization of KIAA gene products
    Takahiro Nagase
    Department of Human Gene Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Brief Funct Genomic Proteomic 5:4-7. 2006
    ..In this review, we describe the current status of the Kazusa mammalian cDNA resources and the future direction of the functional characterization of KIAA genes...
  36. ncbi request reprint Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries
    Noriko Okazaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 10:167-80. 2003
    ..Notably, a homology search against the public database indicated that 4 out of 13 novel cDNA clones were homologous to the disease-related genes...
  37. ncbi request reprint Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21
    M Ohira
    Laboratory of Gene Structure 1, Kazusa DNA Research Institute, Chiba, Japan
    Genome Res 7:47-58. 1997
    ..These nearly full-length cDNA sequences should facilitate understanding of the detailed genome structure of the DS region and help to elucidate their role in the etiology of DS...
  38. ncbi request reprint Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones
    Daisuke Nakajima
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 9:99-106. 2002
    ..The total length of the resultant extensions at amino- and carboxy-terminals of KIAA gene products reached 97,000 and 7,216 amino acid residues, respectively, and various protein domains were found in these extended portions...
  39. ncbi request reprint Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method
    Daisuke Nakajima
    Department of Human Gene Research, Kazusa DNA Research Institute, Kazusa Kamatari, Kisarazu, Chiba, Japan
    DNA Res 12:257-67. 2005
    ....
  40. ncbi request reprint Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones (supplement)
    Daisuke Nakajima
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    DNA Res 9:107-15. 2002
  41. pmc Exploration of human ORFeome: high-throughput preparation of ORF clones and efficient characterization of their protein products
    Takahiro Nagase
    Department of Human Genome Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 15:137-49. 2008
    ..Results thus obtained have demonstrated that our Flexi ORF clones are efficient for the production of HaloTag-fusion proteins that can provide a new versatile set for a variety of functional analyses of human genes...
  42. pmc HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
    Reiko Kikuno
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba, 292 0818, Japan
    Nucleic Acids Res 32:D502-4. 2004
    ..ROUGE summarizes the results of computer-assisted analyses of approximately 1000 mouse homologues of human large cDNAs that we identified...
  43. ncbi request reprint Improvement of recombination efficiency by mutation of red proteins
    Manabu Nakayama
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Biotechniques 38:917-24. 2005
    ..coli chromosome...
  44. ncbi request reprint A system using convertible vectors for screening soluble recombinant proteins produced in Escherichia coli from randomly fragmented cDNAs
    Manabu Nakayama
    Department of Human Gene Research, Kazusa DNA Research Institute, Chiba, Japan
    Biochem Biophys Res Commun 312:825-30. 2003
    ..This high-throughput screening method is particularly useful for procedures that require the handling of many cDNAs in parallel...
  45. ncbi request reprint Influence of the 3'-UTR-length of mKIAA cDNAs and their sequence features to the mRNA expression level in the brain
    Noriko Okazaki
    Kazusa DNA Research Institute, Kazusa Kamatari, Kisarazu, Chiba, Japan
    DNA Res 12:181-9. 2005
    ..Furthermore, we searched sequence elements in the 3'-UTR possibly related with their expression and found some candidates regarding the brain-specific expression...
  46. ncbi request reprint A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: generation and evaluation of anti-mKIAA antibodies
    Hisashi Koga
    Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Proteomics 4:1412-6. 2004
    ..We are currently generating antibody arrays for analysis of protein expression profiles. We will verify protein-protein interactions using immunoprecipitation and tandem mass spectrometry analysis...
  47. ncbi request reprint Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries
    Noriko Okazaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 11:205-18. 2004
    ..Furthermore, 3 out of 4 proteins encoded in the novel cDNA clones showed moderate sequence similarity with human KIAA proteins, thus we could obtain new members of KIAA protein families through our mouse cDNA projects...
  48. ncbi request reprint Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries
    Noriko Okazaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 11:127-35. 2004
    ..Homology and/or motif search against public databases revealed new domains and/or motifs in 26 mFLJ gene products which provide additional speculation regarding the function of FLJ genes...
  49. ncbi request reprint A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins
    Hisashi Koga
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 11:293-304. 2004
    ..This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins...
  50. ncbi request reprint Method for systematic targeted isolation of homologous cDNA fragments in a multiplex format
    Reiko Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    Biotechniques 36:798-800, 802, 804 passim. 2004
    ..We thus expect that this method could be applied to high-throughput cloning of homologous cDNAs in related species...
  51. ncbi request reprint CDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases
    Reiko Ohara
    Department of Human Gene Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
    Biotechniques 38:451-8. 2005
    ..This method enables the construction of a library from a small amount of RNA, and calculations suggest that the strategy would be efficient enough to use even a single cell as starting material...
  52. ncbi request reprint A gene-targeting approach for functional characterization of KIAA genes encoding extremely large proteins
    Manabu Nakayama
    Department of Human Genome Technology, Kausa DNA Research Institute, Japan
    FASEB J 20:1718-20. 2006
    ..Disruption of KIAA1440 led to embryonic lethality at the blastocyst stage. The high success rate of our approach demonstrates the rationale for the genome-wide functional examination of large proteins in mice using reverse genetics...
  53. ncbi request reprint A simple and robust method for preparation of cDNA nylon microarrays
    Hisashi Yamakawa
    Department of Human Gene Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 11:353-60. 2004
    ..The results in this study demonstrate that the introduction of these two modifications in preparation of nylon DNA array greatly improved its quality...
  54. ncbi request reprint DomCut: prediction of inter-domain linker regions in amino acid sequences
    Mikita Suyama
    Laboratory of DNA Technology, Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Bioinformatics 19:673-4. 2003
    ..The prediction is made by using linker index deduced from a data set of domain/linker segments. The linker preference profile, which is the averaged linker index along a sequence, can be visualized in the graphical interface...
  55. pmc Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs
    Manabu Nakayama
    Department of Human Gene Research, Kazusa DNA Research Institute, Kisarazu, Chiba 292 0818, Japan
    Genome Res 12:1773-84. 2002
    ..Our representative library should be a very useful resource for detecting previously unidentified interactions because it complements conventional expression libraries, which seldom contain large cDNAs...
  56. pmc HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
    Reiko Kikuno
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nucleic Acids Res 30:166-8. 2002
    ..More interestingly, in some cases, the ability to compare cDNA with genomic sequences allows us to identify candidate sites of RNA editing. HUGE is available on the World Wide Web at http://www.kazusa.or.jp/huge...
  57. ncbi request reprint A new simplified method for preparation of a synthetic phage antibody with practically acceptable detection sensitivity on immunoblots
    M Nakayama
    Kazusa DNA Research Institute, 1532 3, Yana, Kisarazu, Chiba 292 0812, Japan
    Hum Antibodies 10:55-65. 2001
    ....
  58. ncbi request reprint Kinetic profiles of sequential gene expressions for chemokines in mice with contact hypersensitivity
    Gaku Mitsui
    Department of Human Gene Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba, 292 0818, Japan
    Immunol Lett 86:191-7. 2003
    ....
  59. ncbi request reprint Characterization of long cDNA clones from human adult spleen. II. The complete sequences of 81 cDNA clones
    Hiroyuki Jikuya
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Chiba 292 0818, Japan
    DNA Res 10:49-57. 2003
    ....
  60. doi request reprint Pulse-chase experiment for the analysis of protein stability in cultured mammalian cells by covalent fluorescent labeling of fusion proteins
    Kei Yamaguchi
    Laboratory of Human Gene Research, Department of Human Genome Research, Kazusa DNA Research Institute, Chiba, Japan
    Methods Mol Biol 577:121-31. 2009
    ..Herein, we demonstrated that the method allows analysis of the intracellular protein stability as regulated by protein-degradation signals or an exogenously expressed E3 ubiquitin ligase...
  61. ncbi request reprint Complete sequencing and characterization of 21,243 full-length human cDNAs
    Toshio Ota
    Helix Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Nat Genet 36:40-5. 2004
    ..About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs...
  62. ncbi request reprint An improved cosmid vector for the nested deletion method using the bacteriophage T3 DNA packaging system
    Y Kawarabayasi
    Kazusa DNA Research Institute, Chiba, Japan
    DNA Res 3:37-42. 1996
    ..The cosmid clone constructed by this new vector could be linearized at one of the 8-base cutter sites which are assumed to rarely occur in the genome, and followed by in vitro packaging, nested deletion clones were successfully prepared...
  63. doi request reprint A set of genes associated with the interferon-γ response of lung cancer patients undergoing α-galactosylceramide-pulsed dendritic cell therapy
    Kohsuke Okita
    Department of Immunology, Graduate School of Medicine, Chiba University, Chuo Ku, Chiba, Japan
    Cancer Sci 101:2333-40. 2010
    ..The expression profile of these two genes may be associated with the responsiveness of IFN-γ production after αGalCer-pulsed DC treatment...
  64. ncbi request reprint Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries
    Noriko Okazaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 10:35-48. 2003
    ..Furthermore, we successfully mapped all the mouse KIAA cDNAs along the genome using a recently published mouse genome draft sequence...
  65. ncbi request reprint Effect of a topical steroid on gene expressions for chemokines in mice with contact hypersensitivity
    Gaku Mitsui
    Department of Human Gene Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Int Immunopharmacol 4:57-69. 2004
    ....
  66. ncbi request reprint The Kazusa cDNA project for identification of unknown human transcripts
    Takahiro Nagase
    Department of Human Gene Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    C R Biol 326:959-66. 2003
    ..In the second phase of the project, which aims at bridging the human genome and proteome using the output of the first phase, we are very carefully evaluating our cDNA clones and, when necessary, experimentally revising them...
  67. ncbi request reprint Prediction of the coding sequences of mouse homologues of KIAA gene: I. The complete nucleotide sequences of 100 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries
    Noriko Okazaki
    Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    DNA Res 9:179-88. 2002
    ..The average size of the 100 cDNA sequences reached 5.1 kb and that of mouse KIAA-homologous proteins predicted from these cDNAs was 989 amino acid residues...
  68. ncbi request reprint Towards a proteome project of cyanobacterium Synechocystis sp. strain PCC6803: linking 130 protein spots with their respective genes
    T Sazuka
    Laboratory of DNA Technology, Kazusa DNA Research Institute, Chiba, Japan
    Electrophoresis 18:1252-8. 1997
    ..e., "proteome") of this photosynthetic autotroph. This post-genome project represents a productive way of exploiting the information obtained from the sequencing of the cyanobacterium genome...
  69. ncbi request reprint Mammalian fat3: a large protein that contains multiple cadherin and EGF-like motifs
    Kazutaka Mitsui
    Department of Human Gene Research, Kazusa DNA Research Institute, Chiba ken, Japan
    Biochem Biophys Res Commun 290:1260-6. 2002
    ..These data suggest that the fat3 protein plays an important role in axon fasciculation and modulation of the extracellular space surrounding axons during embryonic development...
  70. ncbi request reprint MEGF1/fat2 proteins containing extraordinarily large extracellular domains are localized to thin parallel fibers of cerebellar granule cells
    Manabu Nakayama
    Kazusa DNA Research Institute, 1532 3 Yana, Kisarazu, Chiba 292 0812, Japan
    Mol Cell Neurosci 20:563-78. 2002
    ..Based on these results, a novel function of the enormous protocadherins in cerebellar development, namely, the modulation of the extracellular space surrounding parallel fibers during development, was proposed...
  71. doi request reprint PCDH24-induced contact inhibition involves downregulation of beta-catenin signaling
    Rui Ose
    Laboratory of Medical Genomics, Department of Human Genome Research, Kazusa DNA Research Institute, 2 6 7 Kazusa Kamatari, Kisarazu, Chiba 292 0818, Japan
    Mol Oncol 3:54-66. 2009
    ..From these findings we propose a novel model for the suppression of beta-catenin signaling by PCDH24 that leads to contact inhibition...
  72. doi request reprint Enhanced Th2 cell differentiation and allergen-induced airway inflammation in Zfp35-deficient mice
    Masayuki Kitajima
    Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
    J Immunol 183:5388-96. 2009
    ..These results indicate that Zfp35 controls Th2 cell differentiation, allergic airway inflammation, and airway hyperresponsiveness in a negative manner. Thus, Zfp35 may control Th2-dependent diseases, such as allergic asthma...
  73. ncbi request reprint Germline mutations of MEK in cardio-facio-cutaneous syndrome are sensitive to MEK and RAF inhibition: implications for therapeutic options
    Thanaset Senawong
    Department of Pathology, School of Medicine, University of California, San Francisco, CA 94143 0128, USA
    Hum Mol Genet 17:419-30. 2008
    ..Thus, regardless of mutations identified in an individual with CFC, MEK inhibition is a potential therapeutic approach for this population...
  74. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  75. doi request reprint Genome-wide identification and characterization of transcripts translationally regulated by bacterial lipopolysaccharide in macrophage-like J774.1 cells
    Hiroshi Kitamura
    Laboratories for Immunogenomics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
    Physiol Genomics 33:121-32. 2008
    ..These results demonstrated that translational suppression may play a critical role in the LPS-mediated attenuation of mitochondrial oxidative phosphorylation in a nitric oxide-independent manner in J774.1 cells...
  76. ncbi request reprint Temporal change in mKIAA gene expression during the early stage of retinoic acid-induced neurite outgrowth
    Kazuhide Imai
    Chiba Industry Advancement Center, 2 6 Nakase, Mihama ku, Chiba 261 7126, Japan
    Gene 364:114-22. 2005
    ..These results indicate that some mKIAA genes are apparently relevant to retinoic acid-induced neurite outgrowth...
  77. pmc The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
    Nucleic Acids Res 36:D793-9. 2008
    ....
  78. pmc Novel regulation of MHC class II function in B cells
    Yohei Matsuki
    Laboratory for Infectious Immunity, RIKEN Research Center for Allergy and Immunology, Tsurumi ku, Yokohama, Kanagawa, Japan
    EMBO J 26:846-54. 2007
    ..These results suggest that the function of MHC II in B cells is regulated through ubiquitination by MARCH-I...
  79. ncbi request reprint Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
    Atsushi Hijikata
    RIKEN Research Center for Allergy and Immunology, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    Bioinformatics 23:2934-41. 2007
    ..To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells...
  80. pmc Development of a microscopic platform for real-time monitoring of biomolecular interactions
    Yasuhiro Sasuga
    The Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    Genome Res 16:132-9. 2006
    ..The unique features of this microbead-based microarray system open the way to explore molecular interactions with a wide range of affinities in extremely small volumes of target solutions, such as extracts from single cells...
  81. pmc Phosphorylation of clock protein PER1 regulates its circadian degradation in normal human fibroblasts
    Koyomi Miyazaki
    Clock Cell Biology Group, IBRF Institute for Biological Resource and Function, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba Central 6, 1 1 1, Higashi, Tsukuba, 305 8566, Japan
    Biochem J 380:95-103. 2004
    ..These findings indicate that circadian hPER1 degradation through a proteasomal pathway can be regulated through phosphorylation by CKI, but not by subcellular localization...
  82. ncbi request reprint High-throughput production of recombinant antigens for mouse KIAA proteins in Escherichia coli: computational allocation of possible antigenic regions, and construction of expression plasmids of glutathione-S-transferase-fused antigens by an in vitro reco
    Yasuhiro Hara
    Chiba Industry Advancement Center, 2 6 Nakase, Mihama ku, Chiba 261 7126, Japan
    DNA Res 10:129-36. 2003
    ..Using these systems, we successfully produced and purified 400 antigens for production of mKIAA antibodies to date...
  83. ncbi request reprint Characterization of mammalian synemin, an intermediate filament protein present in all four classes of muscle cells and some neuroglial cells: co-localization and interaction with type III intermediate filament proteins and keratins
    Yoshiaki Hirako
    Unit of Biosystems, Graduate School of Human Informatics, Nagoya University, Nagoya, Japan
    Cell Tissue Res 313:195-207. 2003
    ..The fact that synemin is present in all four classes of muscle cells and a specific type of glial cells is indicative of important functions. Its incorporation may give structural and functional versatility to the IF cytoskeleton...
  84. pmc Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1
    Shang Yi Chiu
    Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, New York 14642, USA
    RNA 9:77-87. 2003
    ..These data indicate that hSmg5/7a targets protein phosphatase 2A to Upf1 but not Upf2. Results of Western blotting reveal that hSmg5/7a is mostly cytoplasmic in HEK293T cells...
  85. ncbi request reprint A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate
    Mads Grønborg
    Department of Biochemistry and Molecular Biology, Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Mol Cell Proteomics 1:517-27. 2002
    ..Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways...
  86. ncbi request reprint A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling
    Akhilesh Pandey
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 277:19131-8. 2002
    ..This report therefore implicates SLAP and SLAP-2 as a family of adapter proteins that negatively regulate T cell receptor signaling...
  87. ncbi request reprint Intracellular cell-autonomous association of Notch and its ligands: a novel mechanism of Notch signal modification
    Kei Sakamoto
    Department of Oral Restitution, Graduate School, Bunkyo ku, Tokyo 113 8549, Japan
    Dev Biol 241:313-26. 2002
    ....
  88. ncbi request reprint Novel alternative splicings of BPAG1 (bullous pemphigoid antigen 1) including the domain structure closely related to MACF (microtubule actin cross-linking factor)
    Masayo Okumura
    Unit of Biosystems, Graduate School of Human Informatics, Nagoya University, Nagoya 464 8601, Japan
    J Biol Chem 277:6682-7. 2002
    ..The results indicate that BPAG1 has three kinds of cytoskeletal binding domains and seems to play an important role in linking the different types of cytoskeletons...
  89. ncbi request reprint SigC, the group 2 sigma factor of RNA polymerase, contributes to the late-stage gene expression and nitrogen promoter recognition in the cyanobacterium Synechocystis sp. strain PCC 6803
    Munehiko Asayama
    Laboratory of Molecular Genetics, College of Agriculture, Ibaraki University, Inashiki, Japan
    Biosci Biotechnol Biochem 68:477-87. 2004
    ..DNase I footprinting also indicated binding and related sites of NtcA and/or RNAP with SigC on the nitrogen promoter. The unique promoter architecture and the mechanism of transcription by RNAP with SigC are also discussed...
  90. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  91. pmc Isolation from cochlea of a novel human intronless gene with predominant fetal expression
    Barbara L Resendes
    Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital, Boston, MA 02115, USA
    J Assoc Res Otolaryngol 5:185-202. 2004
    ....
  92. ncbi request reprint Utilization of mammalian cells for efficient and reliable evaluation of specificity of antibodies to unravel the cellular function of mKIAA proteins
    Akiyuki Ozaki
    Department of Biotechnology, Institute of Research and Innovation, 1201 Takada, Kashiwa, Chiba 277 0861, Japan
    Gene 360:35-44. 2005
    ..Importantly, these methods allow us to detect potential posttranslational modification of the mKIAA/KIAA proteins and to predict their biological function based on their subcellular localization...
  93. ncbi request reprint The N-terminal domain of MYO18A has an ATP-insensitive actin-binding site
    Yasushi Isogawa
    Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Tokyo 153 8902, Japan
    Biochemistry 44:6190-6. 2005
    ..These results imply that this dimeric myosin might stably cross-link actin filaments by two ATP-insensitive actin-binding sites at the N-terminal domains for higher-order organization of the actin cytoskeleton...
  94. ncbi request reprint Construction of a multi-functional cDNA library specific for mouse pancreatic islets and its application to microarray
    Motoi Nishimura
    Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1 8 1 Inohana, Chuo Ku, Chiba 260 8670, Japan
    DNA Res 11:315-23. 2004
    ..The mouse pancreatic islet cDNA library, sequence database, set of clones, and microarrays developed in this study should be useful resources for studies of pancreatic islets and related diseases including diabetes mellitus...
  95. ncbi request reprint Human ATP-binding cassette transporter ABCC10: expression profile and p53-dependent upregulation
    Shin ichiro Takayanagi
    Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B 60 Nagatsuta, Midori ku, Yokohama 226 8501, Japan
    J Exp Ther Oncol 4:239-46. 2004
    ..These results suggest that expression of the ABCC10 gene is regulated in a p53-dependent manner during DNA-damage-related apoptosis...
  96. ncbi request reprint Post-transcriptional effects of phorbol 12-myristate 13-acetate on transcriptome of U937 cells
    Hiroshi Kitamura
    Laboratory for Immunogenomics, Research Center for Allergy and Immunology, The Institute of Physical and Chemical Research, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    FEBS Lett 578:180-4. 2004
    ..7% of detectable genes in U937 cells. Thus, besides transcriptional modulation by PMA, changes in the translational state of transcripts seem to play a critical role in PMA-induced differentiation of U937 cells...
  97. ncbi request reprint Alternative splice variants encoding unstable protein domains exist in the human brain
    Keiichi Homma
    Laboratory of Gene Product Informatics, Center for Information Biology DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411 8540, Japan
    J Mol Biol 343:1207-20. 2004
    ..We propose that most unstable proteins encoded by alternative splice variants lack normal functions and are an evolutionary dead-end...
  98. ncbi request reprint [Preparation of DNA and RNA]
    Hiroshi Kitamura
    Tanpakushitsu Kakusan Koso 49:1469-75. 2004
  99. ncbi request reprint Mammalian Polycomb Scmh1 mediates exclusion of Polycomb complexes from the XY body in the pachytene spermatocytes
    Yuki Takada
    RIKEN Research Center for Allergy and Immunology, 1 7 22 Suehiro, Yokohama, Japan
    Development 134:579-90. 2007
    ..Therefore, for the first time, we are able to indicate a functional involvement of Prc1 during the meiotic prophase of male germ cells and a regulatory role of Scmh1 for Prc1, which involves sex chromosomes...
  100. doi request reprint Smurf1 directly targets hPEM-2, a GEF for Cdc42, via a novel combination of protein interaction modules in the ubiquitin-proteasome pathway
    Kei Yamaguchi
    Graduate School of Science and Technology, Chiba University, 648 Matsudo, Matsudo, Chiba 271 8510, Japan
    Biol Chem 389:405-13. 2008
    ..Our discovery that hPEM-2 is, in addition to RhoA, a target protein of Smurf1 suggests that Smurf1 plays a crucial role in the spatiotemporal regulation of Rho GTPase family members...