Hiromi Nishida

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113 8657, Japan
    Open Biol 2:120043. 2012
  2. pmc Conservation of nucleosome positions in duplicated and orthologous gene pairs
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    ScientificWorldJournal 2012:298174. 2012
  3. doi request reprint Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
    Genomics 98:370-5. 2011
  4. pmc Genome-wide maps of mononucleosomes and dinucleosomes containing hyperacetylated histones of Aspergillus fumigatus
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    PLoS ONE 5:e9916. 2010
  5. doi request reprint Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
    Hiromi Nishida
    Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    Bioinformatics 25:2295-7. 2009
  6. doi request reprint An epigenetic aberration increased in intergenic regions of cloned mice
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, Yokohama, Japan
    Mamm Genome 19:667-74. 2008
  7. ncbi request reprint Evolution of gamma-butyrolactone synthases and receptors in Streptomyces
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    Environ Microbiol 9:1986-94. 2007
  8. ncbi request reprint Phylogenetic and disruption analyses of aspartate kinase of Deinococcus radiodurans
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
    Biosci Biotechnol Biochem 71:1015-20. 2007
  9. ncbi request reprint Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunyo ku, Tokyo, Japan
    Biosci Biotechnol Biochem 70:2646-52. 2006
  10. ncbi request reprint Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Yokohama, Japan
    Chromosome Res 14:203-11. 2006

Collaborators

Detail Information

Publications33

  1. pmc Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113 8657, Japan
    Open Biol 2:120043. 2012
    ..We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome...
  2. pmc Conservation of nucleosome positions in duplicated and orthologous gene pairs
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    ScientificWorldJournal 2012:298174. 2012
    ..7). The absence of nucleosome position conservation in promoters of orthologous genes suggests organismal specificity of nucleosome arrangements...
  3. doi request reprint Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
    Genomics 98:370-5. 2011
    ..Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae...
  4. pmc Genome-wide maps of mononucleosomes and dinucleosomes containing hyperacetylated histones of Aspergillus fumigatus
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    PLoS ONE 5:e9916. 2010
    ..However, most of the nucleosome positions are conserved in the gene promoters, even after treatment with TSA, because of the low density of nucleosomes in the gene promoters...
  5. doi request reprint Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
    Hiromi Nishida
    Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    Bioinformatics 25:2295-7. 2009
    ..Our findings strongly suggest that the nucleosomes protecting longer DNA fragments against MNase at the promoters, thereby inhibiting high gene expression...
  6. doi request reprint An epigenetic aberration increased in intergenic regions of cloned mice
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, Yokohama, Japan
    Mamm Genome 19:667-74. 2008
    ....
  7. ncbi request reprint Evolution of gamma-butyrolactone synthases and receptors in Streptomyces
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    Environ Microbiol 9:1986-94. 2007
    ..This idea is consistent with the diverged combination of AfsA homologues and ArpA homologues in a Streptomyces strain...
  8. ncbi request reprint Phylogenetic and disruption analyses of aspartate kinase of Deinococcus radiodurans
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
    Biosci Biotechnol Biochem 71:1015-20. 2007
    ..A D. radiodurans AK disruption mutant exhibited a phenotype similar to a T. thermophilus AK disruption mutant, which indicates that these two AKs have different evolutionary origins, though their functions are not different...
  9. ncbi request reprint Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunyo ku, Tokyo, Japan
    Biosci Biotechnol Biochem 70:2646-52. 2006
    ..cerevisiae produces novel proteins and that ancestral fungi also produced small proteins most of which have disappeared or have been combined with other proteins during fungal evolution...
  10. ncbi request reprint Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Yokohama, Japan
    Chromosome Res 14:203-11. 2006
    ..Our results imply that the relative nucleosome depletion in the vicinity of TSS is not necessarily associated with active transcription, but with histone H3 K9 acetylation in promoter...
  11. pmc Comparative analysis of expression of histone H2a genes in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 6:108. 2005
    ..In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation)--quantitative PCR (qPCR) analysis...
  12. pmc Molecular evolution of adenylating domain of aminoadipate reductase
    Kwang Deuk An
    Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
    BMC Evol Biol 3:9. 2003
    ..In this study, we aimed to determine which bacterial adenylating domain is most closely related to Lys2. In addition, we analyzed the substitution rate of the adenylating domain-encoding region...
  13. doi request reprint Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria
    Masaki Shintani
    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
    Plasmid 66:85-92. 2011
    ..These differences may have resulted in distinct behaviors of the plasmid or of its host strain, and RNA maps of pCAR1 give us important information to understand the plasmid behaviors in different environments...
  14. doi request reprint Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1
    Masaki Shintani
    Biotechnology Research Center, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    Environ Microbiol 12:1413-26. 2010
    ..Our findings indicate that the possession of pCAR1 altered the growth rate of the host via the expression of genes on pCAR1 and the host chromosomes...
  15. pmc Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function
    Choong Soo Yun
    Biotechnology Research Center and Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    J Bacteriol 192:4720-31. 2010
    ..Our findings indicate that Pmr is a key factor in optimizing gene transcription on pCAR1 and the host chromosome...
  16. pmc Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiae
    Takashi Matsumoto
    Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
    PLoS ONE 6:e16372. 2011
    ..Interestingly, in 19 of the 24 genes, the profiles of nucleosome mapping numbers were similar between the two disruptants...
  17. pmc High-resolution mapping of plasmid transcriptomes in different host bacteria
    Masatoshi Miyakoshi
    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
    BMC Genomics 10:12. 2009
    ..Although the transcription pattern of genes on a plasmid can be altered by a change in host background, the expression range of plasmid genes that will result in phenotypic variation has not been quantitatively investigated...
  18. doi request reprint Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus
    Takuya Ouchi
    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
    Nat Chem Biol 9:277-83. 2013
    ..Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX...
  19. pmc Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:23. 2005
    ..In the present study, we evaluated this transcript by using RT-PCR and compared the expression patterns of the sense and antisense transcripts by using quantitative RT-PCR (qRT-PCR)...
  20. ncbi request reprint Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparison
    Wellyzar Sjamsuridzal
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    J Gen Appl Microbiol 48:121-3. 2002
  21. pmc A novel replication-independent histone H2a gene in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:10. 2005
    ..The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR...
  22. pmc Distribution of introns in fungal histone genes
    Choong Soo Yun
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
    PLoS ONE 6:e16548. 2011
    ....
  23. doi request reprint Phylogenetic analyses of phytoplasmas based on whole-genome comparison
    Hiromi Nishida
    Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
    Methods Mol Biol 938:319-27. 2013
    ..However, horizontal gene transfer has occurred rarely during the evolution of Mollicutes. Thus, the two phylogenetic topologies of the Mollicutes based on the two different strategies are similar...
  24. doi request reprint Symbiobacterium lost carbonic anhydrase in the course of evolution
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, 113 8657, Japan
    J Mol Evol 68:90-6. 2009
    ..thermophilum and several related organisms lost this enzyme during the course of evolution. The loss of CA could be based on the availability of a high level of CO(2) in their living environments...
  25. doi request reprint Detection of the genes evolving under Ureaplasma-specific selection
    Kenro Oshima
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    J Mol Evol 66:529-32. 2008
    ..This raises the possibility that Ureaplasma does not need a glycolysis pathway for ATP synthesis. This unique energy-producing system may be related to the Ureaplasma-specific evolution of the glycolytic genes...
  26. pmc Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons
    Kenro Oshima
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    Int J Evol Biol 2011:376831. 2011
    ..Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription...
  27. ncbi request reprint Phylogenetic relationships among mycoplasmas based on the whole genomic information
    Kenro Oshima
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
    J Mol Evol 65:249-58. 2007
    ..The phylogenetic approaches at the whole-genome level are very important and will be essential for microbial evolutionary studies...
  28. ncbi request reprint Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans
    Hiromi Nishida
    Institute of Molecular and Cellular Biosciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Microbiology 148:2911-4. 2002
    ..Each disruptant of DR1420 and DR1758, and of DR1420 or DR1758 grew in a minimal medium, as did the wild-type. These results show that D. radiodurans performs lysine biosynthesis in a unique way...
  29. pmc Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses
    Kwang Deuk An
    Institute of Molecular and Cellular Biosciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    BMC Evol Biol 2:6. 2002
    ..In this study, we designed degenerate primers for polymerase chain reaction (PCR) amplification of a large fragment of the aminoadipate reductase gene for divergent fungi...
  30. doi request reprint Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113 8657, Japan
    Gene 525:5-10. 2013
    ..nidulans and A. oryzae. These results strongly suggest that the GC content in the exons of the orthologous gene pairs has been conserved during evolution but the nucleosome density has varied throughout...
  31. pmc Evolution of lysine biosynthesis in the phylum deinococcus-thermus
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    Int J Evol Biol 2012:745931. 2012
    ..Phylogenetic analyses of D. proteolyticus lysine biosynthetic genes showed that the key gene cluster for the DAP pathway was transferred horizontally from a phylogenetically distant organism...
  32. pmc Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes
    Hiromi Nishida
    Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 8657, Japan
    Int J Evol Biol 2011:634505. 2011
    ..After acquiring genes, Symbiobacterium increased the GC content of the horizontally transferred genes and thereby maintained a genome with a high GC content...
  33. ncbi request reprint Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells
    Hiroyuki Sobajima
    Biotechnology Research Center, The University of Tokyo, Tokyo 113 8657, Japan
    Planta 216:692-8. 2003
    ..Thus the rice enzyme was termed OsOPR1. The physiological roles of OsOPR1 are discussed. This is the first report of the cloning of an OPR gene from a monocot plant...