start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue=1 article-no= start-page=18550 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20201029 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Topoisomerase II beta targets DNA crossovers formed between distant homologous sites to induce chromatin opening en-subtitle= kn-subtitle= en-abstract= kn-abstract=Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T- segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be derived from distant sites on the same chromosome. Due to lack of proper methodology, however, no direct evidence has been described so far. The beta isoform of topo II (topo II beta) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. Here we devise a genome-wide mapping technique (eTIP-seq) for topo II beta target sites that can measure the genomic distance between G- and T-segments. It revealed that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that topo II beta acts on crossovers to unknot the intertwined DSP sites, leading to chromatin decondensation. en-copyright= kn-copyright= en-aut-name=MiyajiMary en-aut-sei=Miyaji en-aut-mei=Mary kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=FurutaRyohei en-aut-sei=Furuta en-aut-mei=Ryohei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HosoyaOsamu en-aut-sei=Hosoya en-aut-mei=Osamu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=SanoKuniaki en-aut-sei=Sano en-aut-mei=Kuniaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=HaraNorikazu en-aut-sei=Hara en-aut-mei=Norikazu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KuwanoRyozo en-aut-sei=Kuwano en-aut-mei=Ryozo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=KangJiyoung en-aut-sei=Kang en-aut-mei=Jiyoung kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=TatenoMasaru en-aut-sei=Tateno en-aut-mei=Masaru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TsutsuiKimiko M. en-aut-sei=Tsutsui en-aut-mei=Kimiko M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=TsutsuiKen en-aut-sei=Tsutsui en-aut-mei=Ken kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=5 en-affil=Department of Molecular Genetics, Bioresource Science Branch, Center for Bioresources, Brain Research Institute, Niigata University kn-affil= affil-num=6 en-affil=Department of Molecular Genetics, Bioresource Science Branch, Center for Bioresources, Brain Research Institute, Niigata University kn-affil= affil-num=7 en-affil=Graduate School of Life Science, University of Hyogo kn-affil= affil-num=8 en-affil=Graduate School of Life Science, University of Hyogo kn-affil= affil-num=9 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= affil-num=10 en-affil=Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University kn-affil= en-keyword=Biochemistry kn-keyword=Biochemistry en-keyword=Molecular biology kn-keyword=Molecular biology END start-ver=1.4 cd-journal=joma no-vol=42 cd-vols= no-issue=14 article-no= start-page=9005 end-page=9020 dt-received= dt-revised= dt-accepted= dt-pub-year=2014 dt-pub=20140717 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Nuclear dynamics of topoisomerase II beta reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain en-subtitle= kn-subtitle= en-abstract= kn-abstract=DNA topoisomerase II (topo II) changes DNA topology by cleavage/re-ligation cycle(s) and thus contributes to various nuclear DNA transactions. It is largely unknown how the enzyme is controlled in a nuclear context. Several studies have suggested that its C-terminal domain (CTD), which is dispensable for basal relaxation activity, has some regulatory influence. In this work, we examined the impact of nuclear localization on regulation of activity in nuclei. Specifically, human cells were transfected with wild-type and mutant topo II beta tagged with EGFP. Activity attenuation experiments and nuclear localization data reveal that the endogenous activity of topo II beta is correlated with its subnuclear distribution. The enzyme shuttles between an active form in the nucleoplasm and a quiescent form in the nucleolus in a dynamic equilibrium. Mechanistically, the process involves a tethering event with RNA. Isolated RNA inhibits the catalytic activity of topo II beta in vitro through the interaction with a specific 50-residue region of the CTD (termed the CRD). Taken together, these results suggest that both the subnuclear distribution and activity regulation of topo II beta are mediated by the interplay between cellular RNA and the CRD. en-copyright= kn-copyright= en-aut-name=OnodaAkihisa en-aut-sei=Onoda en-aut-mei=Akihisa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HosoyaOsamu en-aut-sei=Hosoya en-aut-mei=Osamu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SanoKuniaki en-aut-sei=Sano en-aut-mei=Kuniaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KiyamaKazuko en-aut-sei=Kiyama en-aut-mei=Kazuko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=KimuraHiroshi en-aut-sei=Kimura en-aut-mei=Hiroshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KawanoShinji en-aut-sei=Kawano en-aut-mei=Shinji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=FurutaRyohei en-aut-sei=Furuta en-aut-mei=Ryohei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MiyajiMary en-aut-sei=Miyaji en-aut-mei=Mary kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TsutsuiKen en-aut-sei=Tsutsui en-aut-mei=Ken kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=TsutsuiKimiko M. en-aut-sei=Tsutsui en-aut-mei=Kimiko M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=2 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=3 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=4 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=5 en-affil= kn-affil=Osaka Univ, Grad Sch Frontier Biosci, Lab Biol Sci affil-num=6 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=7 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=8 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=9 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen affil-num=10 en-affil= kn-affil=Okayama Univ, Grad Sch Med Dent & Pharmaceut Sci, Dept Neurogen END start-ver=1.4 cd-journal=joma no-vol=59 cd-vols= no-issue=4 article-no= start-page=113 end-page=120 dt-received= dt-revised= dt-accepted= dt-pub-year=2005 dt-pub=200508 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Dynamic view of the nuclear matrix. en-subtitle= kn-subtitle= en-abstract= kn-abstract=

The nuclear matrix is an operationally defined nuclear skeletal structure that is believed to be involved in many nuclear functions including DNA replication, transcription, repair, and prem RNA processing/transport. Until relatively recently, the nuclear matrix was thought to be a rigid and static structure, but it is now thought to be dynamic. This paradigm shift was based in part on the tracking of the intranuclear movement of proteins tagged with fluorochromes. In this review, we attempt to redefine the nuclear matrix in light of recent findings and describe some useful techniques for the dynamic analysis of nuclear function.

en-copyright= kn-copyright= en-aut-name=TsutsuiKimiko M. en-aut-sei=Tsutsui en-aut-mei=Kimiko M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SanoKuniaki en-aut-sei=Sano en-aut-mei=Kuniaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TsutsuiKen en-aut-sei=Tsutsui en-aut-mei=Ken kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil= kn-affil=Okayama University affil-num=2 en-affil= kn-affil=Okayama University affil-num=3 en-affil= kn-affil=Okayama University en-keyword=nuclear matrix kn-keyword=nuclear matrix en-keyword=MAR kn-keyword=MAR en-keyword=chromatin kn-keyword=chromatin en-keyword=histone modification kn-keyword=histone modification en-keyword=topoisomerase kn-keyword=topoisomerase END start-ver=1.4 cd-journal=joma no-vol=121 cd-vols= no-issue=3 article-no= start-page=143 end-page=147 dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=20091201 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=DNA topoisomerase Uβ activates a subset of neuronal genes kn-title=DNAトポイソメラーゼUβによる神経関連遺伝子の活性化機構 en-subtitle= kn-subtitle= en-abstract= kn-abstract= en-copyright= kn-copyright= en-aut-name=SanoKuniaki en-aut-sei=Sano en-aut-mei=Kuniaki kn-aut-name=佐野訓明 kn-aut-sei=佐野 kn-aut-mei=訓明 aut-affil-num=1 ORCID= en-aut-name=MiyajiMary en-aut-sei=Miyaji en-aut-mei=Mary kn-aut-name=宮地まり kn-aut-sei=宮地 kn-aut-mei=まり aut-affil-num=2 ORCID= en-aut-name=TsutsuiM. Kimiko en-aut-sei=Tsutsui en-aut-mei=M. Kimiko kn-aut-name=筒井公子 kn-aut-sei=筒井 kn-aut-mei=公子 aut-affil-num=3 ORCID= en-aut-name=TsutsuiKen en-aut-sei=Tsutsui en-aut-mei=Ken kn-aut-name=筒井研 kn-aut-sei=筒井 kn-aut-mei=研 aut-affil-num=4 ORCID= affil-num=1 en-affil= kn-affil=岡山大学大学院医歯薬学総合研究科　神経ゲノム学 affil-num=2 en-affil= kn-affil=岡山大学大学院医歯薬学総合研究科　神経ゲノム学 affil-num=3 en-affil= kn-affil=岡山大学大学院医歯薬学総合研究科　神経ゲノム学 affil-num=4 en-affil= kn-affil=岡山大学大学院医歯薬学総合研究科　遺伝情報動態学 en-keyword=DNAトポイソメラーゼUβ　(DNA topoisomeraseUbeta) kn-keyword=DNAトポイソメラーゼUβ　(DNA topoisomeraseUbeta) en-keyword=神経細胞分化 (neuronal differentiation) kn-keyword=神経細胞分化 (neuronal differentiation) en-keyword=遺伝子発現 (gene expression) kn-keyword=遺伝子発現 (gene expression) en-keyword=神経関連遺伝子 (neuronal gene) kn-keyword=神経関連遺伝子 (neuronal gene) en-keyword=クロマチン (chromatin) kn-keyword=クロマチン (chromatin) END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=1997 dt-pub=19970325 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=脳由来神経栄養因子BDNF遺伝子の細胞内カルシウム流入による発現誘導機構の解析 en-subtitle= kn-subtitle= en-abstract= kn-abstract= en-copyright= kn-copyright= en-aut-name= en-aut-sei= en-aut-mei= kn-aut-name=佐野訓明 kn-aut-sei=佐野 kn-aut-mei=訓明 aut-affil-num=1 ORCID= affil-num=1 en-affil= kn-affil=岡山大学 END