Takashi Ohyama
Waseda University
Eukaryotic transcriptionPromoterGeneBiophysicsMolecular biologyDNA supercoilgenomic DNAChemistryPlasmidTranscription (biology)GeneticsDNABiochemistryHistoneTATA boxComputational biologyChromatinNucleosomeBiologyCell biology
89Publications
17H-index
869Citations
Publications 90
Newest
#2Osamu Miura (Waseda University)H-Index: 2
Last. Takashi OhyamaH-Index: 17
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DNA can adopt various structures besides the B-form. Among them, cruciform structures are formed on inverted repeat (IR) sequences. While cruciform formable IRs (CFIRs) are sometimes found in regulatory regions of transcription, their function in transcription remains elusive, especially in eukaryotes. We found a cluster of CFIRs within the mouse Pou5f1 enhancer. Here, we demonstrate that this cluster or some member(s) plays an active role in the transcriptional regulation of not only Pou5f1, bu...
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#1Naoki Arai (Waseda University)H-Index: 3
#2Yusuke Ohno (Waseda University)
Last. Takashi Ohyama (Waseda University)H-Index: 17
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Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports o...
6 CitationsSource
#1Osamu Miura (Waseda University)H-Index: 2
#2Toshihiro Ogake (Waseda University)H-Index: 1
Last. Takashi Ohyama (Waseda University)H-Index: 17
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DNA sequences that read the same from 5′ to 3′ in either strand are called inverted repeat sequences or simply IRs. They are found throughout a wide variety of genomes, from prokaryotes to eukaryotes. Despite extensive research, their in vivo functions, if any, remain unclear. Using Saccharomyces cerevisiae, we performed genome-wide analyses for the distribution, occurrence frequency, sequence characteristics and relevance to chromatin structure, for the IRs that reportedly have a cruciform-form...
2 CitationsSource
#1Osamu Miura (Waseda University)H-Index: 2
#2Toshihiro Ogake (Waseda University)H-Index: 1
Last. Takashi Ohyama (Waseda University)H-Index: 17
view all 3 authors...
Inverted repeat (IR) sequences are DNA sequences that read the same from 5′ to 3′ in each strand. Some IRs can form cruciforms under the stress of negative supercoiling, and these IRs are widely found in genomes. However, their biological significance remains unclear. The aim of the current study is to explore this issue further. We constructed the first Escherichia coli genome-wide comprehensive map of IRs with cruciform-forming potential. Based on the map, we performed detailed and quantitativ...
2 CitationsSource
#1Hiroyuki Komatsu (TUT: Toyohashi University of Technology)H-Index: 2
#2Junya Yamamoto (TUT: Toyohashi University of Technology)H-Index: 2
Last. Yo Kikuchi (TUT: Toyohashi University of Technology)H-Index: 14
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: The marine bacterium Rhodovulum sulfidophilum is a nonsulfur phototrophic bacterium, which is known to produce extracellular nucleic acids in soluble form in culture medium. In the present paper, constructing the response regulator ctrA-deficient mutant of R. sulfidophilum, we found that this mutation causes a significant decrease in the extracellular DNA production. However, by the introduction of a plasmid containing the wild type ctrA gene into the mutant, the amount of extracellular DNA pr...
2 CitationsSource
#1Osamu MiuraH-Index: 31
#2Toshihiro OgakeH-Index: 1
Last. Takashi OhyamaH-Index: 17
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Last. Takashi OhyamaH-Index: 17
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#1Hiroki YoneyamaH-Index: 1
Last. Takashi OhyamaH-Index: 17
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#1Jun ichi Tanase (Waseda University)H-Index: 4
#2Takehiro Yokoo (Waseda University)H-Index: 1
Last. Takashi Ohyama (Waseda University)H-Index: 17
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Abstract Magnesium chloride and polyamines stabilize DNA and chromatin. Furthermore, they can induce nucleosome aggregation and chromatin condensation in vitro . To determine the effects of elevating the cation concentrations in the nucleus of a living cell, we microinjected various concentrations of mono-, di- and polyvalent cation solutions into the nuclei of mouse embryonic stem (ES) cells and traced their fates. Here, we show that an elevation of either MgCl 2 , spermidine or spermine concen...
1 CitationsSource