Taro Tsujimura

Taro Tsujimura

Core Manager (SignAC)

Junior Associate Professor
Research Field
Genomics and Gene Regulation

Research Overview

3D (epi-)genome at single-cell resolution

My research interest is to understand full spectrum of cis-interaction to gain insights into evolution and human diseases by genomic rearrangements. I have recently developed a system, named STITCH, to control gene-enhancer interaction by drugs (Tsujimura et al. 2020 eLife). Exploiting the unique system, I would like to further dissect out the process of gene activation by long-range enhancers, and how it is regulated in the genome.

The field of epigenomics is being accelerated by rapid revolution of technology to analyze the epigenomic and transcriptomic states of individual cells. I am also engaged in development of novel analytical tools for single-cell epigenomics. Taking advantage of the collaborative environment at ASHBi, I would like to apply these techniques and others for the the studies of myself and others, to establish a cutting-edge concept in the field of human biology.

Fig 1 of Dr Tsujimura's Research

Fig 1: The STITCH control of the gene-enhancer interaction


Taro Tsujimura obtained his PhD from the University of Tokyo for his study in the regulation of tandemly duplicated opsin genes in zebrafish (2008). In 2009, he moved to EMBL Heidelberg in Germany and studied the relationship between genomic organization, chromatin conformation, and enhancer regulation as a postdoc. In 2014, he became a Research Assistant Professor at University of Tokyo Hospital, and then at Keio University School of Medicine until 2019. He is now appointed as Junior Associate Professor at ASHBi, Kyoto University.


Tsujimura T, Takase O, Yoshikawa M, Sano E, Hayashi M, Hoshi K, Takato T, Toyoda A, Okano H, Hishikawa K. Controlling gene activation by enhancers through a drug-inducible topological insulator. Elife. 2020 May 5;9:e47980. doi: 10.7554/eLife.47980. PMID: 32369019; PMCID: PMC7200164.

Tsujimura T, Takase O, Yoshikawa M, Sano E, Hayashi M, Takato T, Toyoda A, Okano H, Hishikawa K. Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus. Epigenetics Chromatin. 2018 Sep 14;11(1):51. doi: 10.1186/s13072-018-0221-1. PMID: 30213272; PMCID: PMC6137755.

Tsujimura T, Idei M, Yoshikawa M, Takase O, Hishikawa K. Roles and regulation of bone morphogenetic protein-7 in kidney development and diseases. World J Stem Cells. 2016 Sep 26;8(9):288-96. doi: 10.4252/wjsc.v8.i9.288. PMID: 27679685; PMCID: PMC5031890.

Tsujimura T, Masuda R, Ashino R, Kawamura S. Spatially differentiated expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. BMC Genet. 2015 Nov 4;16:130. doi: 10.1186/s12863-015-0288-7. PMID: 26537431; PMCID: PMC4634787.

Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F. A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet. 2015 Jan 8;11(1):e1004897. doi: 10.1371/journal.pgen.1004897. PMID: 25569170; PMCID: PMC4288730.

Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014 Mar;24(3):390-400. doi: 10.1101/gr.163519.113. Epub 2014 Jan 7. PMID: 24398455; PMCID: PMC3941104.

Li YN, Tsujimura T, Kawamura S, Dowling JE. Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. J Comp Neurol. 2012 Nov 1;520(16):3786-802. doi: 10.1002/cne.23168. PMID: 22907678; PMCID: PMC3669674.

Tsujimura T, Hosoya T, Kawamura S. A single enhancer regulating the differential expression of duplicated red-sensitive opsin genes in zebrafish. PLoS Genet. 2010 Dec 16;6(12):e1001245. doi: 10.1371/journal.pgen.1001245. PMID: 21187910; PMCID: PMC3002997.

Fukamachi S, Kinoshita M, Tsujimura T, Shimada A, Oda S, Shima A, Meyer A, Kawamura S, Mitani H. Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter. Genetics. 2008 Feb;178(2):761-9. doi: 10.1534/genetics.107.073387. Epub 2008 Feb 1. PMID: 18245373; PMCID: PMC2248340.

Tsujimura T, Chinen A, Kawamura S. Identification of a locus control region for quadruplicated green-sensitive opsin genes in zebrafish. Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12813-8. doi: 10.1073/pnas.0704061104. Epub 2007 Jul 23. PMID: 17646658; PMCID: PMC1937549.


July 2010 Postdoctoral Researcher Travel Award, Annual meeting of the Society of Molecular Biology and Evolution, 2010
June 2008 Final candidate for Walter M. Fitch Student Award, Annual Meeting of the Society of Molecular Biology and Evolution 2008
March 2008 Excellent Doctoral Thesis Award 2008 from Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo
March 2008 Dean Prize, Graduate School of Frontier Sciences (Doctoral Course) 2008 from Graduate School of Frontier Sciences, University of Tokyo


Research Group

Single-Cell Genome Information Analysis Core (SignAC)


Dec. 1, 2019

Contact T.Tsujimura

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