Research Topics
| Hiromi NishidaSummaryAffiliation: University of Tokyo Country: Japan Publications
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Detail Information
Publications
Conservation of nucleosome positions in duplicated and orthologous gene pairsHiromi 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...
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatusHiromi 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...- Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and ThermotogaeHiromi 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... 
Evolution of gamma-butyrolactone synthases and receptors in StreptomycesHiromi 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...- Phylogenetic and disruption analyses of aspartate kinase of Deinococcus radioduransHiromi 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... - Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiaeHiromi 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... - Genome-wide maps of mononucleosomes and dinucleosomes containing hyperacetylated histones of Aspergillus fumigatusHiromi 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... - An epigenetic aberration increased in intergenic regions of cloned miceHiromi Nishida
Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, Yokohama, Japan
Mamm Genome 19:667-74. 2008.... - Comparative analysis of expression of histone H2a genes in mouseHiromi 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... - Molecular evolution of adenylating domain of aminoadipate reductaseKwang 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... - Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteriaMasaki 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... - Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1Masaki 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... - Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cellHiromi 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... - 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 functionChoong 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... - High-resolution mapping of plasmid transcriptomes in different host bacteriaMasatoshi 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... - Lysine and arginine biosyntheses mediated by a common carrier protein in SulfolobusTakuya 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... - Naturally occurring antisense RNA of histone H2a in mouse cultured cell linesHiromi 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)... - Distribution of introns in fungal histone genesChoong Soo Yun
Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
PLoS ONE 6:e16548. 2011.... - A novel replication-independent histone H2a gene in mouseHiromi 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... - Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiaeTakashi 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... - Phylogenetic analyses of phytoplasmas based on whole-genome comparisonHiromi 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... - Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mappingHiromi 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... - Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparisonWellyzar 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 - Symbiobacterium lost carbonic anhydrase in the course of evolutionHiromi 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... - Detection of the genes evolving under Ureaplasma-specific selectionKenro 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... - Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence ComparisonsKenro 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... - Phylogenetic relationships among mycoplasmas based on the whole genomic informationKenro 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... - Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radioduransHiromi 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... - Evolution of lysine biosynthesis in the phylum deinococcus-thermusHiromi 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... - Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cellsHiroyuki 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... - Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum GenesHiromi 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... - Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analysesKwang 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...