News
Research
Members
Publications
Access
Gallery
Search
Cell_Tokyo_Tech?lang=ja Hiroshi@Cell_Tokyo_Tech
Tokyo Institute of Technology
 
English
日本語
       
 
  　　Selected Papers
　　Academic Society
  Link：T2R2 Tokyo Tech Research Repository, Google scholar,
Research map
 
 
 

【Selected Papers】

  1. Tjalsma SJD, Hori M, Sato Y, Bousard A, Ohi A, Raposo AC, Roensch J, Le Saux A, Nogami J, Maehara K, Kujirai T, Handa T, Bagés-Arnal S, Ohkawa Y, Kurumizaka H, da Rocha ST, Żylicz JJ, Kimura H, Heard E. H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing. EMBO Rep 22: e51989 (2021)
  2. Handa T, Harada A, Maehara K, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y, Kimura H. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input. Nature Protocols 15: 3334–3360 (2020)
  3. Hayashi-Takanaka Y, Kina Y, Nakamura F, Becking LE, Nakao Y, Nagase T, Nozaki N, Kimura H. Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis. J Cell Sci 133: jcs243444 (2020)
  4. Sato Y, Hilbert L, Oda H, Wan Y, Heddleston JM, Chew TL, Zaburdaev V, Keller P, Lionnet T, Vastenhouw N, Kimura H. Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis. Development 146, dev179127 (2019)
  5. Chung CI, Sato Y, Ohmuro-Mutsuyama Y, Machida S, Kurumizaka H, Kimura H, Ueda H. Intrabody-based FRET probe to visualize endogenous histone acetylation. Sci Rep 9, 10188 (2019)
  6. Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, Sato Y, Kimura H, Stasevich TJ. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nature Commun 10(1), 2947 (2019)
  7. Hayashi-Takanaka Y, Kina Y, Nakamura F, Yamazaki S, Harata M, Soest RWMV, Kimura H, Nakao Y. Effect of mycalolides isolated from a marine sponge Mycale aff. nullarosette on actin in living cells. Sci Rep 9, 7540 (2019)
  8. Yamagata K, Nagai K, Miyamoto H, Anzai M, Kato H, Miyamoto K, Kurosaka S, Azuma R, Kolodeznikov II, Protopopov AV, Plotnikov VV, Kobayashi H, Kawahara-Miki R, Kono T, Uchida M, Shibata Y, Handa T, Kimura H, Hosoi Y, Mitani T, Matsumoto K, Iritani A. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Sci Rep 9, 4050 (2019)
  9. Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y. A chromatin integration labelling method enables epigenomic profiling with lower input. Nature Cell Biol 2, 7 (2019)
  10. Sato Y, Stasevich TJ, Kimura H. Visualizing the Dynamics of Inactive X Chromosomes in Living Cells Using Antibody-Based Fluorescent Probes. X-Chromosome Inactivation 91-102 (2018)
  11. Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, Ohkawa Y. Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration Nature Commun 9(1), 1400 (2018)
  12. Sato Y, Kimura H. Semi-quantitative Analysis of H4K20me1 Levels in Living Cells Using Mintbody. bio-protocol 7(10), e2276, 10 (2017)
  13. Yamazaki T, Hatano Y, Handa T, Kato S, Hoida K, Yamamura R, Fukuyama T, Uematsu T, Kobayashi N, Kimura H, Yamagata K. Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase. PLoS One 12(5), e0177764 (2017)
  14. Kurita K, Sakamoto T, Yagi N, Sakamoto Y, Ito A, Nishino N, Sako K, Yoshida M, Kimura H, Seki M, Matsunaga S. Live imaging of H3K9 acetylation in plant cells. Sci Rep 7,45894 (2017)
  15. Sato Y, Kujirai T, Arai R, Asakawa H, Ohtsuki C, Horikoshi N, Yamagata K, Ueda J, Nagase T, Haraguchi T, Hiraoka Y, Kimura A, Kurumizaka H, Kimura H. A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation. J Mol Biol 428(20), 3385-3902 (2016)
  16. Kaimori JY, Maehara K, Hayashi-Takanaka Y, Harada A, Fukuda M, Yamamoto S, Ichimaru N, Umehara T, Yokoyama S, Matsuda R, Ikura T, Nagao K, Obuse C, Nozaki N, Takahara S, Takao T, Ohkawa Y, Kimura H, Isaka Y. Histone H4 lysine 20 acetylation is associated with gene repression in human cells. Sci Rep 6, 24318 (2016)
  17. Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells. eLife 4, e11215 (2015)
  18. Hayashi-Takanaka Y, Maehara K, Harada A, Umehara T, Yokoyama S, Obuse C, Ohkawa Y, Nozaki N, Kimura H. Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies. Chromosome Res 23(4), 753-766 (2015)
  19. Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, and Kimura H. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516, 272-275 (2014)
  20. Stasevich TJ, Sato Y, Nozaki N, and Kimura H. Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells. Methods 70(2-3), 77-88 (2014)
  21. Hayashi-Takanaka Y, Stasevich TJ, Kurumizaka H, Nozaki N, and Kimura H. Evaluation of chemical fluorescent dyes as a protein conjugation partner for live cell imaging. PLoS One 9, e106271 (2014)
  22. Jullien J, Miyamoto K, Pasque V, Allen GE, Bradshaw CR, Garrett NJ, Halley-Stott RP, Kimura H, Ohsumi K, Gurdon JB. Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming. Mol Cell 55, 524-536 (2014)
  23. Zierhut C, Jenness C, Kimura H, and Funabiki H. Nucleosomal regulation of chromatin composition and nuclear assembly revealed by histone depletion. Nature Struct Mol Biol 21, 617-625 (2014)
  24. Hori T, Shang WH, Toyoda A, Misu S, Monma N, Ikeo K, Molina O, Vargiu G, Fujiyama A, Kimura H, Earnshaw WC, and Fukagawa T. Histone H4 Lys 20 mono-methylation of the CENP-A nucleosome is essential for kinetochore assembly. Dev Cell 29, 740-749 (2014)
  25. Ueda J, Maehara K, Mashiko D, Ichinose T, Yao T, Hori M, Sato Y, Kimura H, Ohkawa Y, Yamagata K. Heterochromatin Dynamics during the Differentiation Process Revealed by the DNA Methylation Reporter Mouse, MethylRO. Stem Cell Reports 2, 910?924 (2014)
  26. Baba T, Otake H, Sato T, Miyabayashi K, Shishido Y, Wang CY, Shima Y, Kimura H, Yagi M, Ishihara Y, Hino S, Ogawa H, Nakao M, Yamazaki T, Kang D, Ohkawa Y, Suyama M, Chung BC, Morohashi K. Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1. Nature Commun 5, 3634 (2014)
  27. Arimura Y, Kimura H, Oda T, Sato K, Osakabe A, Tachiwana H, Sato Y, Kinugasa Y, Ikura T, Sugiyama M, Sato M, and Kurumizaka H. Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin. Sci Rep 3, 3510 (2013)
  28. Sato Y, Mukai M, Ueda J, Muraki M, Stasevich TJ, Horikoshi N, Kujirai T, Kita H, Kimura T, Hira S, Okada Y, Hayashi-Takanaka Y, Obuse C, Kurumizaka H, Kawahara A, Yamagata K, Nozaki N, and Kimura H. Genetically encoded system to track histone modification in vivo. Sci Rep 3, 2436 (2013)
  29. Sadaie M, Salma R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Perez-Mancera, Bennett DC, Chong H, Kimura H, and Narita M. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev 27, 1800-1808 (2013)
  30. Shang WH, Hori T, Martins NM, Toyoda A, Misu S, Monma N, Hiratani I, Maeshima K, Ikeo K, Fujiyama A, Kimura H, Earnshaw WC, and Fukagawa T. Chromosome engineering allows the efficient isolation of vertebrate neocentromeres. Dev Cell 24, 635-648 (2013)
  31. Nozawa RS, Nagao K, Igami K, Shibata S, Shirai N, Nozaki N, Sado T, Kimura H, and Obuse C. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1?HBiX1 pathway. Nature Struct Mol Biol 20, 566-573 (2013)
  32. Kimura H. Histone modification for human epigenome analysis. J Hum Genet 58, 439-445 (2013)
  33. Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, N?nez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavare S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, and Narita M. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell 47, 203-214 (2012)
  34. Hayashi-Takanaka Y, Yamagata K, Wakayama T, Stasevich TJ, Kainuma T, Tsurimoto T, Tachibana M, Shinkai Y, Kurumizaka H, Nozaki N, and Kimura H. Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling. Nucleic Acids Res 39, 6475-6488 (2011)
  35. Kelly AE, Ghenoiu C, Xue JZ, Zierhut C, Kimura H, and Funabiki H. Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. Science 330, 235-239 (2010)
  36. Nozawa RS, Nagao K, Masuda HT, Iwasaki O, Hirota T, Nozaki N, Kimura H, and Obuse C. Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation. Nature Cell Biol 12, 719-727 (2010)
  37. Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, and Kurumizaka H. Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc Natl Acad Sci USA 107, 10454-10459 (2010)
  38. Matsui T, Leung D, Miyashita H, Maksakova IA, Miyachi H, Kimura H, Tachibana M, *Lorincz MC, and Shinkai Y. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464, 927-931 (2010)
  39. Kimura H, Hayashi-Takanaka Y, and Yamagata K. Visualization of DNA methylation and histone modifications in living cells. Curr Opin Cell Biol 22, 412-418 (2010)
  40. Hayashi-Takanaka Y, Yamagata K, Nozaki N, and Kimura H. Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase. J Cell Biol 187, 781-790 (2009)
  41. Goto Y and Kimura H. Inactive X chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene. Nucleic Acids Res 37, 7416-7428 (2009)
  42. Kimura H, Hayashi-Takanaka Y, Goto Y, Takizawa N, and Nozaki N. The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct Funct 33, 61-73 (2008)
  43. Kimura H, Takizawa N, Allemand E, Hori T, Iborra FJ, Nozaki N, Muraki M, Hagiwara M, Krainer AR, Fukagawa T, and Okawa K. A novel histone exchange factor, protein phosphatase 2Cgamma, mediates the exchange and dephosphorylation of H2A-H2B. J Cell Biol 175, 389-400 (2006)
  44. Kimura H. Histone dynamics in living cells revealed by photobleaching. DNA Repair 4, 939-950 (2005)
  45. Kimura H, Sugaya K, and Cook PR. The transcription cycle of RNA polymerase II in living cells. J Cell Biol 159, 777-782 (2002)
  46. Kimura H and Cook PR. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol 153, 1341-1353 (2001)
  47. Kimura H, Tao Y, Roeder RG, and Cook PR. Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol Cell Biol 19, 5383-5392 (1999)
  48. Kimura H, Ohtomo T, Yamaguchi M, Ishii A, and Sugimoto K. Mouse MCM proteins: complex formation and transportation to the nucleus. Genes Cells 1, 977-993 (1996)
  49. Kimura H, Takizawa N, Nozaki N, and Sugimoto K. Molecular cloning of cDNA encoding mouse Cdc21 and CDC46 homologs and characterization of the products: physical interaction between P1(MCM3) and CDC46 proteins. Nucleic Acids Res 23, 2097-2104 (1995)
  50. Kimura H, Nozaki N, and Sugimoto K. DNA polymerase alpha associated protein P1, a murine homolog of yeast MCM3, changes its intranuclear distribution during the DNA synthetic period. EMBO J 13, 4311-4320 (1994)
  ▲TOP
 
 

【Academic Society】

　　　The Molecular Biology Society of Japan
　　　Japan Society for Cell Biology (councillor)
　　　The Biophysical Society of Japan
　　　The Japanese Society for Epigenetics (secretary)
  ▲TOP