Osamu Nishimura - RIKEN BDR

Updated on Nov 13, 2023

西村　理		Osamu Nishimura, Ph.D.

理化学研究所生命機能科学研究センター (BDR)		RIKEN Center for Biosystems Dynamics Research (BDR)
発生ゲノムシステム研究チーム		Laboratory for Developmental Genome System

Academic Degree

Doctor of Science (Kyoto University)
博士（理学）・京都大学

Doctor thesis:
Insights into brain evolution and asexual-sexual cycle from the genome analysis of the planarian Dugesia japonica
プラナリアDugesia japonicaのゲノム解析による、脳の進化および無性／有性生殖サイクルに関する考察

Supervisor:
Prof. Kiyokazu Agata, Department of Biophysics, Graduate School of Science, Kyoto University
京都大学大学院理学研究科生物科学専攻生物物理学教室阿形清和教授

Original Papers (Peer Reviewed)

[61]
Bilgic M, Wu Q, Suetsugu T, Shitamukai A, Tsunekawa Y, Shimogori T, Kadota M, Nishimura O, Kuraku S, Kiyonari H, Matsuzaki F.
Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals
eLife 2023 12:RP91406

[60]
Enomoto Y, Katsura H, Fujimura T, Ogata A, Baba S, Yamaoka A, Kihara M, Abe T, Nishimura O, Kadota M, Hazama D, Tanaka Y, Maniwa Y, Nagano T, Morimoto M.
Autocrine TGF-β-positive feedback in profibrotic AT2-lineage cells plays a crucial role in non-inflammatory lung fibrogenesis.
Nat Commun. 2023 Aug 31;14(1):4956. doi: 10.1038/s41467-023-40617-y. PMID: 37653024; PMCID: PMC10471635.

[59]
Yamaguchi K, Uno Y, Kadota M, Nishimura O, Nozu R, Murakumo K, Matsumoto R, Sato K, Kuraku S.
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.
Genome Res. 2023 Sep;33(9):1527-1540. doi: 10.1101/gr.276840.122. Epub 2023 Aug 17. PMID: 37591668; PMCID: PMC10620051.

[58]
Sakaguchi S, Mizuno S, Okochi Y, Tanegashima C, Nishimura O, Uemura T, Kadota M, Naoki H, Kondo T.
Single-cell transcriptome atlas of Drosophila gastrula 2.0.
Cell Rep. 2023 Jul 25;42(7):112707. doi: 10.1016/j.celrep.2023.112707. Epub 2023 Jul 10. PMID: 37433294.

[57]
Nakayama M, Nishimura O, Nishimura Y, Kitaichi M, Kuraku S, Sone M, Hama C.
Control of Synaptic Levels of Nicotinic Acetylcholine Receptor by the Sequestering Subunit Dα5 and Secreted Scaffold Protein Hig.
J Neurosci. 2023 May 31;43(22):3989-4004. doi: 10.1523/JNEUROSCI.2243-21.2023. Epub 2023 Apr 28. PMID: 37117011; PMCID: PMC10255049.

[56]
Hiver S, Shimizu-Mizuno N, Ikawa Y, Kajikawa E, Sai X, Nishimura H, Takaoka K, Nishimura O, Kuraku S, Tanaka S, Hamada H.
Gse1, a component of the CoREST complex, is required for placenta development in the mouse.
Dev Biol. 2023 Apr 3:S0012-1606(23)00052-0. doi: 10.1016/j.ydbio.2023.03.009. Epub ahead of print. PMID: 37019373.

[55]
Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S.
Squalomix: shark and ray genome analysis consortium and its data sharing platform
F1000Res. 2022 Sep 21;11:1077. doi: 10.12688/f1000research.123591.1. PMID: 36262334; PMCID: PMC9561540.

[54]
Kabir A, Ieda R, Hosoya S, Fujikawa D, Atsumi K, Tajima S, Nozawa A, Koyama T, Hirase S, Nakamura O, Kadota M, Nishimura O, Kuraku S, Nakamura Y, Kobayashi H, Toyoda A, Tasumi S, Kikuchi K.
Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish.
Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2121469119. doi: 10.1073/pnas.2121469119. Epub 2022 Jun 3. PMID: 35658077.

[53]
Yamaguchi K, Kadota M, Nishimura O, Ohishi Y, Naito Y, Kuraku S.
Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies.
Mol Ecol. 2021 Aug 25. doi: 10.1111/mec.16146. Epub ahead of print. PMID: 34432923.

[52]
Jayakumar V, Nishimura O, Kadota M, Hirose N, Sano H, Murakawa Y, Yamamoto Y, Nakaya M, Tsukiyama T, Seita Y, Nakamura S, Kawai J, Sasaki E, Ema M, Kuraku S, Kawaji H, Sakakibara Y.
Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset.
Sci Data. 2021 Jun 28;8(1):159. doi: 10.1038/s41597-021-00935-6. PMID: 34183680; PMCID: PMC8239027.

[51]
Fujimoto S, Yamanaka K, Tanegashima C, Nishimura O, Kuraku S, Kuratani S, Irie N.
Measuring potential effects of the developmental burden associated with the vertebrate notochord.
J Exp Zool B Mol Dev Evol. 2021 Mar 10. doi: 10.1002/jez.b.23032. PMID: 33689235.

[50]
Onimaru K, Tatsumi K, Tanegashima C, Kadota M, Nishimura O, Kuraku S.
Developmental hourglass and heterochronic shifts in fin and limb development.
Elife. 2021 Feb 9;10:e62865. doi: 10.7554/eLife.62865. PMID: 33560225; PMCID: PMC7932699.

[49]
Auwal MA, Kashima M, Nishimura O, Hosoda K, Motoishi M, Kamimura A, Okumura A, Agata K, Umesono Y.
Identification and characterization of a fibroblast growth factor gene in the planarian Dugesia japonica.
Dev Growth Differ. 2020 Oct 20. doi: 10.1111/dgd.12696. PMID: 33080046.

[48]
Kusakabe R, Higuchi S, Tanaka M, Kadota M, Nishimura O, Kuratani S
Novel developmental bases for the evolution of hypobranchial muscles in vertebrates.
BMC Biol. 2020 Sep 09;18(1):120

[47]
Onimaru K, Nishimura O, Kuraku S
Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information
PLoS One.. 2020 Jul 23;15(7):e0235748. doi: 10.1371/journal.pone.0235748. eCollection 2020.

[46]
Kadota M*, Nishimura O*, Miura H, Tanaka K, Hiratani I, Kuraku S.
* These authors contributed equally to the work.
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
Gigascience. 2020 Jan 1;9(1). pii: giz158. doi: 10.1093/gigascience/giz158.

[45]
Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanagi M, Keeley SD, Tatsumi K, Tanaka K, Motone F, Kageyama Y, Nozu R, Adachi N, Nishimura O, Nakagawa R, Tanegashima C, Kiyatake I, Matsumoto R, Murakumo K, Nishida K, Terakita A, Kuratani S, Sato K, Hyodo S, Kuraku S
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates
Nat Ecol Evol. 2018 Nov; 2(11):1761-1771

[44]
Tanegashima C, Nishimura O, Motone F, Tatsumi K, Kadota M, Kuraku S
Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei
Sci Data. 2018 Oct 8;5:180200. doi: 10.1038/sdata.2018.200.

[43]
Nabeshima R, Nishimura O, Maeda T, Shimizu N, Ide T, Yashiro K, Sakai Y, Meno C, Kadota K, Shiratori H, Kuraku S, Hamada H
Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters
eLife. 2018 Aug 2;7. pii: e36435. doi: 10.7554/eLife.36435.

[42]
Hosoda K, Motoishi M, Kunimoto T, Nishimura O, Hwang B, Kobayashi S, Yazawa S, Mochii M, Agata K, Umesono Y
Role of MEKK1 in the anterior-posterior patterning during planarian regeneration
Dev Growth Differ. 2018 Jun. doi: 10.1111/dgd.12541.

[41]
Nishimura O, Hara Y, Kuraku S
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Bioinformatics. 2017; 33(22):3635-3637. [ gVolante Server ]

[40]
Kadota M, Hara Y, Tanaka K, Takagi W, Tanegashima C, Nishimura O, Kuraku S
CTCF binding landscape in jawless fish with reference to Hox cluster evolution
Sci Rep. 2017 Jul 10;7(1):4957

[39]
Okashita N, Suwa Y, Nishimura O, Sakashita N, Kadota M, Nagamatsu G, Kawaguchi M, Kashida H, Nakajima A, Tachibana M, Seki Y
PRDM14 drives OCT3/4 recruitment via active demethylation in the transition from primed to naive pluripotency
Stem Cell Rep. 2016 Dec 13;7(6):1072-1086

[38]
Teramoto M, Kudome T, Nishimura O, An Y, Kashima M, Shibata N, Agata K
Molecular markers for X-ray-insensitive differentiated cells in the inner and outer regions of the mesenchymal space in planarian
Dev Growth Differ, 2016, Sep;58(7):609-19.

[37]
Shibata N, Kashima M, Ishiko T, Nishimura O, Rouhana L, Misaki K, Yonemura S, Saito K, Siomi H, Siomi Mikiko C, Agata K:
Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian.
Developmental Cell 2016, 37:226-237.

[36]
Hosoda K, Morimoto M, Motoishi M, Nishimura O, Agata K, Umesono Y:
A simple blood-feeding method for live imaging of gut tube remodeling in regenerating planarians.
Dev Growth Differ, 2016, 58:260-269.

[35]
Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, Perrin D, Fujishima H, Ukai H, Nishimura O, Shi S, Ohno R, Narumi R, Shimizu Y, Tone D, Ode KL, Kuraku S, Ueda HR:
Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene.
Cell Rep, 2016, 14:662-677.

[34]
Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K:
Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica.
PLoS ONE, 2015, 10(11):e0143525.

[33]
Tatsumi K, Nishimura O, Itomi K, Tanegashima C, Kuraku S:
Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.
Biotechniques 2014, 58:253-257.

[32]
Sakamaki K, Shimizu K, Iwata H, Imai K, Satou Y, Funayama N, Nozaki M, Yajima M, Nishimura O, Higuchi M, et al:
The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution.
Mol Biol Evol 2014, 31:3282-3301.

[31]
Uesaka M, Nishimura O, Go Y, Nakashima K, Agata K, Imamura T:
Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals.
BMC Genomics 2014, 15:35.

[30]
Fujimaki K, Fujisawa T, Yazawa S, Nishimura O, Sota T:
Comparative transcriptomic analysis of two closely related ground beetle species with marked genital divergence using pyrosequencing.
Zoolog Sci 2014, 31:587-592.

[29]
B. Islam F, Uno Y, Nunome M, Nishimura O, Tarui H, Agata K, Matsuda Y:
Comparison of the Chromosome Structures between the Chicken and Three Anserid Species, the Domestic Duck (Anas platyrhynchos), Muscovy Duck (Cairina moschata), and Chinese Goose (Anser cygnoides), and the Delineation of their Karyotype Evolution by Comparative Chromosome Mapping.
The Journal of Poultry Science 2014, 51:1-13.

[28]
Umesono Y, Tasaki J, Nishimura Y, Hrouda M, Kawaguchi E, Yazawa S, Nishimura O, Hosoda K, Inoue T, Agata K:
The molecular logic for planarian regeneration along the anterior-posterior axis.
Nature 2013, 500:73-76.

[27]
Toju H, Sato H, Yamamoto S, Kadowaki K, Tanabe AS, Yazawa S, Nishimura O, Agata K:
How are plant and fungal communities linked to each other in belowground ecosystems? A massively parallel pyrosequencing analysis of the association specificity of root-associated fungi and their host plants.
Ecol Evol 2013, 3:3112-3124.

[26]
Kuraku S, Zmasek CM, Nishimura O, Katoh K:
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
Nucleic Acids Res 2013, 41:W22-28.

[25]
Uno Y, Nishida C, Tarui H, Ishishita S, Takagi C, Nishimura O, Ishijima J, Ota H, Kosaka A, Matsubara K, et al:
Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping.
PLoS One 2012, 7:e53027.

[24]
Shibata N, Hayashi T, Fukumura R, Fujii J, Kudome-Takamatsu T, Nishimura O, Sano S, Son F, Suzuki N, Araki R, et al:
Comprehensive gene expression analyses in pluripotent stem cells of a planarian, Dugesia japonica.
Int J Dev Biol 2012, 56:93-102.

[23]
Sakurai T, Lee H, Kashima M, Saito Y, Hayashi T, Kudome-Takamatsu T, Nishimura O, Agata K, Shibata N:
The planarian P2X homolog in the regulation of asexual reproduction.
Int J Dev Biol 2012, 56:173-182.

[22]
Ozawa R, Nishimura O, Yazawa S, Muroi A, Takabayashi J, Arimura G:
Temperature-dependent, behavioural, and transcriptional variability of a tritrophic interaction consisting of bean, herbivorous mite, and predator.
Mol Ecol 2012, 21:5624-5635.

[21]
Nishimura O, Hirao Y, Tarui H, Agata K:
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species.
BMC Genomics 2012, 13:289.

[20]
Nishimura O, Brillada C, Yazawa S, Maffei ME, Arimura G:
Transcriptome pyrosequencing of the parasitoid wasp Cotesia vestalis: genes involved in the antennal odorant-sensory system.
PLoS One 2012, 7:e50664.

[19]
Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y:
Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake.
BMC Genomics 2012, 13:604.

[18]
Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, Toyoda A, Fujiyama A, Agata K, Fuse N:
Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.
PLoS One 2012, 7:e33288.

[17]
Tasaki J, Shibata N, Nishimura O, Itomi K, Tabata Y, Son F, Suzuki N, Araki R, Abe M, Agata K, Umesono Y:
ERK signaling controls blastema cell differentiation during planarian regeneration.
Development 2011, 138:2417-2427.

[16]
Takechi M, Takeuchi M, Ota KG, Nishimura O, Mochii M, Itomi K, Adachi N, Takahashi M, Fujimoto S, Tarui H, et al:
Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa.
J Exp Zool B Mol Dev Evol 2011, 316:526-546.

[15]
Kanayama M, Akiyama-Oda Y, Nishimura O, Tarui H, Agata K, Oda H:
Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation.
Nat Commun 2011, 2:500.

[14]
Hayashi T, Motoishi M, Yazawa S, Itomi K, Tanegashima C, Nishimura O, Agata K, Tarui H:
A LIM-homeobox gene is required for differentiation of Wnt-expressing cells at the posterior end of the planarian body.
Development 2011, 138:3679-3688.

[13]
Rouhana L, Shibata N, Nishimura O, Agata K:
Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance.
Dev Biol 2010, 341:429-443.

[12]
Maki N, Suetsugu-Maki R, Sano S, Nakamura K, Nishimura O, Tarui H, Del Rio-Tsonis K, Ohsumi K, Agata K, Tsonis PA:
Oocyte-type linker histone B4 is required for transdifferentiation of somatic cells in vivo.
FASEB J 2010, 24:3462-3467.

[11]
Maki N, Martinson J, Nishimura O, Tarui H, Meller J, Tsonis PA, Agata K:
Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags.
Mol Vis 2010, 16:72-78.

[10]
Hayashi T, Shibata N, Okumura R, Kudome T, Nishimura O, Tarui H, Agata K:
Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell research.
Dev Growth Differ 2010, 52:131-144.

[9]
Eto K, Eda K, Hayano M, Goto S, Nagao K, Kawasaki T, Kashimura H, Tarui H, Nishimura O, Agata K, Abe S:
Reduced expression of an RNA-binding protein by prolactin leads to translational silencing of programmed cell death protein 4 and apoptosis in newt spermatogonia.
J Biol Chem 2009, 284:23260-23271.

[8]
Egger B, Steinke D, Tarui H, De Mulder K, Arendt D, Borgonie G, Funayama N, Gschwentner R, Hartenstein V, Hobmayer B, Hooge M, Hrouda M, Ishida S, Kobayashi C, Kuales G, Nishimura O, et al:
To be or not to be a flatworm: the acoel controversy.
PLoS One 2009, 4:e5502.

[7]
Yamamoto S, Nishimura O, Misaki K, Nishita M, Minami Y, Yonemura S, Tarui H, Sasaki H:
Cthrc1 selectively activates the planar cell polarity pathway of Wnt signaling by stabilizing the Wnt-receptor complex.
Dev Cell 2008, 15:23-36.

[6]
Oral O, Uchida I, Eto K, Nakayama Y, Nishimura O, Hirao Y, Ueda J, Tarui H, Agata K, Abe S:
Promotion of spermatogonial proliferation by neuregulin 1 in newt (Cynops pyrrhogaster) testis.
Mech Dev 2008, 125:906-917.

[5]
Higuchi S, Hayashi T, Tarui H, Nishimura O, Nishimura K, Shibata N, Sakamoto H, Agata K:
Expression and functional analysis of musashi-like genes in planarian CNS regeneration.
Mech Dev 2008, 125:631-645.

[4]
Oda H, Nishimura O, Hirao Y, Tarui H, Agata K, Akiyama-Oda Y:
Progressive activation of Delta-Notch signaling from around the blastopore is required to set up a functional caudal lobe in the spider Achaearanea tepidariorum.
Development 2007, 134:2195-2205.

[3]
Ishizuka H, Maezawa T, Kawauchi J, Nodono H, Hirao Y, Nishimura O, Nakagawa H, Sekii K, Tasaka K, Tarui H, et al:
The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive system.
Zoolog Sci 2007, 24:31-37.

[2]
Matsuda Y, Nishida-Umehara C, Tarui H, Kuroiwa A, Yamada K, Isobe T, Ando J, Fujiwara A, Hirao Y, Nishimura O, et al:
Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other.
Chromosome Res 2005, 13:601-615.

[1]
Minami Y, Nishimura O, Hara-Nishimura I, Nishimura M, Matsubara H:
Tissue and intracellular localization of indican and the purification and characterization of indican synthase from indigo plants.
Plant Cell Physiol 2000, 41:218-225.

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