Yokomori, Kyoko

Title(s)Professor, Biological Chemistry
Phone(949) 824-8215, 2158
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    Collapse Research 
    Collapse Research Activities and Funding
    Genetic and epigenetic mechamisms of FSHD pathogenesis
    NIH/NIAMS R01AR071287Sep 1, 2017 - Aug 31, 2022
    Role: Principal Investigator
    Single-nucleus profiling of FSHD heterogeneity
    NIH/NIAMS R21AR071104Apr 1, 2017 - Mar 31, 2019
    Role: Principal Investigator
    Analysis of D4Z4 heterochromatin in FSHD myoblast models
    NIH/NIAMS R21AR067636Feb 13, 2015 - Jan 31, 2017
    Role: Principal Investigator
    Nipbl haploinsufficiency in Cornelia de Lange Syndrome
    NIH/NICHD R21HD078849May 5, 2014 - Apr 30, 2016
    Role: Principal Investigator
    Role of Cohesin in Developmental Gene Regulation
    NIH/NICHD R21HD062951Feb 1, 2010 - Jan 31, 2012
    Role: Principal Investigator
    Epigenomic Analysis of Facioscapulohumeral Muscular Dystrophy
    NIH/NIAMS R01AR058548Sep 1, 2009 - Aug 31, 2014
    Role: Principal Investigator
    Role of Human Condensin in DNA repair
    NIH/NIEHS R21ES013511Dec 30, 2004 - Nov 30, 2007
    Role: Principal Investigator
    Molecular mechanism of DNA damage recognition in mammals
    NIH/NCI R01CA100710Jul 1, 2004 - Apr 30, 2010
    Role: Principal Investigator
    NIH/NIGMS R01GM059150May 1, 1999 - Apr 30, 2004
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Kong X, Cruz GMS, Trinh SL, Zhu XD, Berns MW, Yokomori K. Biphasic recruitment of TRF2 to DNA damage sites promotes non-sister chromatid homologous recombination repair. J Cell Sci. 2018 Dec 05; 131(23). PMID: 30404833.
      View in: PubMed
    2. Kong X, Cruz GMS, Silva BA, Wakida NM, Khatibzadeh N, Berns MW, Yokomori K. Laser Microirradiation to Study In Vivo Cellular Responses to Simple and Complex DNA Damage. J Vis Exp. 2018 01 31; (131). PMID: 29443023.
      View in: PubMed
    3. Newkirk DA, Chen YY, Chien R, Zeng W, Biesinger J, Flowers E, Kawauchi S, Santos R, Calof AL, Lander AD, Xie X, Yokomori K. The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome. Clin Epigenetics. 2017; 9:89. PMID: 28855971.
      View in: PubMed
    4. Kong X, Ball AR, Yokomori K. The Use of Laser Microirradiation to Investigate the Roles of Cohesins in DNA Repair. Methods Mol Biol. 2017; 1515:227-242. PMID: 27797083.
      View in: PubMed
    5. Zeng W, Jiang S, Kong X, El-Ali N, Ball AR, Ma CI, Hashimoto N, Yokomori K, Mortazavi A. Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. Nucleic Acids Res. 2016 12 01; 44(21):e158. PMID: 27566152.
      View in: PubMed
    6. Saquilabon Cruz GM, Kong X, Silva BA, Khatibzadeh N, Thai R, Berns MW, Yokomori K. Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites. Nucleic Acids Res. 2016 Feb 18; 44(3):e27. PMID: 26424850; PMCID: PMC4756852.
    7. Spitler R, Ho H, Norpetlian F, Kong X, Jiang J, Yokomori K, Andersen B, Boss GR, Berns MW. Combination of low level light therapy and nitrosyl-cobinamide accelerates wound healing. J Biomed Opt. 2015 May; 20(5):051022. PMID: 25562608; PMCID: PMC4284311.
    8. Kline AD, Calof AL, Lander AD, Gerton JL, Krantz ID, Dorsett D, Deardorff MA, Blagowidow N, Yokomori K, Shirahige K, Santos R, Woodman J, Megee PC, O'Connor JT, Egense A, Noon S, Belote M, Goodban MT, Hansen BD, Timmons JG, Musio A, Ishman SL, Bryan Y, Wu Y, Bettini LR, Mehta D, Zakari M, Mills JA, Srivastava S, Haaland RE. Clinical, developmental and molecular update on Cornelia de Lange syndrome and the cohesin complex: abstracts from the 2014 Scientific and Educational Symposium. Am J Med Genet A. 2015 Jun; 167(6):1179-92. PMID: 25899772.
      View in: PubMed
    9. Tuzon CT, Spektor T, Kong X, Congdon LM, Wu S, Schotta G, Yokomori K, Rice JC. Concerted activities of distinct H4K20 methyltransferases at DNA double-strand breaks regulate 53BP1 nucleation and NHEJ-directed repair. Cell Rep. 2014 Jul 24; 8(2):430-8. PMID: 25001286; PMCID: PMC4134327.
    10. Hinde E, Kong X, Yokomori K, Gratton E. Chromatin dynamics during DNA repair revealed by pair correlation analysis of molecular flow in the nucleus. Biophys J. 2014 Jul 01; 107(1):55-65. PMID: 24988341; PMCID: PMC4119266.
    11. Silva BA, Stambaugh JR, Yokomori K, Shah JV, Berns MW. DNA damage to a single chromosome end delays anaphase onset. J Biol Chem. 2014 Aug 15; 289(33):22771-84. PMID: 24982423; PMCID: PMC4132783.
    12. Zeng W, Chen YY, Newkirk DA, Wu B, Balog J, Kong X, Ball AR, Zanotti S, Tawil R, Hashimoto N, Mortazavi A, van der Maarel SM, Yokomori K. Genetic and epigenetic characteristics of FSHD-associated 4q and 10q D4Z4 that are distinct from non-4q/10q D4Z4 homologs. Hum Mutat. 2014 Aug; 35(8):998-1010. PMID: 24838473; PMCID: PMC4489691.
    13. Hinde E, Yokomori K, Gaus K, Hahn KM, Gratton E. Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. Sci Rep. 2014 Feb 27; 4:4219. PMID: 24573109; PMCID: PMC3936235.
    14. Kline AD, Calof AL, Schaaf CA, Krantz ID, Jyonouchi S, Yokomori K, Gauze M, Carrico CS, Woodman J, Gerton JL, Vega H, Levin AV, Shirahige K, Champion M, Goodban MT, O'Connor JT, Pipan M, Horsfield J, Deardorff MA, Ishman SL, Dorsett D. Cornelia de Lange syndrome: further delineation of phenotype, cohesin biology and educational focus, 5th Biennial Scientific and Educational Symposium abstracts. Am J Med Genet A. 2014 Jun; 164A(6):1384-93. PMID: 24504889.
      View in: PubMed
    15. Kong X, Ball AR, Pham HX, Zeng W, Chen HY, Schmiesing JA, Kim JS, Berns M, Yokomori K. Distinct functions of human cohesin-SA1 and cohesin-SA2 in double-strand break repair. Mol Cell Biol. 2014 Feb; 34(4):685-98. PMID: 24324008; PMCID: PMC3911484.
    16. Ball AR, Chen YY, Yokomori K. Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. Biochim Biophys Acta. 2014 Mar; 1839(3):191-202. PMID: 24269489; PMCID: PMC3951616.
    17. Spitler R, Schwappacher R, Wu T, Kong X, Yokomori K, Pilz RB, Boss GR, Berns MW. Nitrosyl-cobinamide (NO-Cbi), a new nitric oxide donor, improves wound healing through cGMP/cGMP-dependent protein kinase. Cell Signal. 2013 Dec; 25(12):2374-82. PMID: 23920342.
      View in: PubMed
    18. Wu N, Kong X, Ji Z, Zeng W, Potts PR, Yokomori K, Yu H. Scc1 sumoylation by Mms21 promotes sister chromatid recombination through counteracting Wapl. Genes Dev. 2012 Jul 01; 26(13):1473-85. PMID: 22751501; PMCID: PMC3403015.
    19. Balog J, Thijssen PE, de Greef JC, Shah B, van Engelen BG, Yokomori K, Tapscott SJ, Tawil R, van der Maarel SM. Correlation analysis of clinical parameters with epigenetic modifications in the DUX4 promoter in FSHD. Epigenetics. 2012 Jun 01; 7(6):579-84. PMID: 22522912; PMCID: PMC3398987.
    20. Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X. AREM: aligning short reads from ChIP-sequencing by expectation maximization. J Comput Biol. 2011 Nov; 18(11):1495-505. PMID: 22035330; PMCID: PMC3216101.
    21. Chien R, Zeng W, Ball AR, Yokomori K. Cohesin: a critical chromatin organizer in mammalian gene regulation. Biochem Cell Biol. 2011 Oct; 89(5):445-58. PMID: 21851156; PMCID: PMC4056987.
    22. Kong X, Stephens J, Ball AR, Heale JT, Newkirk DA, Berns MW, Yokomori K. Condensin I recruitment to base damage-enriched DNA lesions is modulated by PARP1. PLoS One. 2011; 6(8):e23548. PMID: 21858164; PMCID: PMC3155556.
    23. Ball AR, Yokomori K. Damage site chromatin: open or closed? Curr Opin Cell Biol. 2011 Jun; 23(3):277-83. PMID: 21489773; PMCID: PMC3109140.
    24. Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR, Calof AL, Lander AD, Groudine MT, Yokomori K. Cohesin mediates chromatin interactions that regulate mammalian ß-globin expression. J Biol Chem. 2011 May 20; 286(20):17870-8. PMID: 21454523; PMCID: PMC3093862.
    25. Wu S, Wang W, Kong X, Congdon LM, Yokomori K, Kirschner MW, Rice JC. Dynamic regulation of the PR-Set7 histone methyltransferase is required for normal cell cycle progression. Genes Dev. 2010 Nov 15; 24(22):2531-42. PMID: 20966048; PMCID: PMC2975929.
    26. Gomez-Godinez V, Wu T, Sherman AJ, Lee CS, Liaw LH, Zhongsheng Y, Yokomori K, Berns MW. Analysis of DNA double-strand break response and chromatin structure in mitosis using laser microirradiation. Nucleic Acids Res. 2010 Dec; 38(22):e202. PMID: 20923785; PMCID: PMC3001094.
    27. Zeng W, Ball AR, Yokomori K. HP1: heterochromatin binding proteins working the genome. Epigenetics. 2010 May 16; 5(4):287-92. PMID: 20421743; PMCID: PMC3103764.
    28. Yusufzai T, Kong X, Yokomori K, Kadonaga JT. The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA. Genes Dev. 2009 Oct 15; 23(20):2400-4. PMID: 19793863; PMCID: PMC2764493.
    29. Kawauchi S, Calof AL, Santos R, Lopez-Burks ME, Young CM, Hoang MP, Chua A, Lao T, Lechner MS, Daniel JA, Nussenzweig A, Kitzes L, Yokomori K, Hallgrimsson B, Lander AD. Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/-) mouse, a model of Cornelia de Lange Syndrome. PLoS Genet. 2009 Sep; 5(9):e1000650. PMID: 19763162; PMCID: PMC2730539.
    30. Stephens J, Mohanty SK, Genc S, Kong X, Yokomori K, Berns MW. Spatially sculpted laser scissors for study of DNA damage and repair. J Biomed Opt. 2009 Sep-Oct; 14(5):054004. PMID: 19895106; PMCID: PMC2774973.
    31. Zeng W, de Greef JC, Chen YY, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 2009 Jul; 5(7):e1000559. PMID: 19593370; PMCID: PMC2700282.
    32. Ball AR, Yokomori K. Revisiting the role of heterochromatin protein 1 in DNA repair. J Cell Biol. 2009 May 18; 185(4):573-5. PMID: 19451270; PMCID: PMC2711565.
    33. Kong X, Mohanty SK, Stephens J, Heale JT, Gomez-Godinez V, Shi LZ, Kim JS, Yokomori K, Berns MW. Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells. Nucleic Acids Res. 2009 May; 37(9):e68. PMID: 19357094; PMCID: PMC2685111.
    34. Kong X, Ball AR, Sonoda E, Feng J, Takeda S, Fukagawa T, Yen TJ, Yokomori K. Cohesin associates with spindle poles in a mitosis-specific manner and functions in spindle assembly in vertebrate cells. Mol Biol Cell. 2009 Mar; 20(5):1289-301. PMID: 19116315.
      View in: PubMed
    35. Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, Cobb BS, Yokomori K, Dillon N, Aragon L, Fisher AG, Merkenschlager M. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell. 2008 Feb 08; 132(3):422-33. PMID: 18237772.
      View in: PubMed
    36. Ball AR, Yokomori K. Damage-induced reactivation of cohesin in postreplicative DNA repair. Bioessays. 2008 Jan; 30(1):5-9. PMID: 18081005; PMCID: PMC4127326.
    37. Murakawa Y, Sonoda E, Barber LJ, Zeng W, Yokomori K, Kimura H, Niimi A, Lehmann A, Zhao GY, Hochegger H, Boulton SJ, Takeda S. Inhibitors of the proteasome suppress homologous DNA recombination in mammalian cells. Cancer Res. 2007 Sep 15; 67(18):8536-43. PMID: 17875693.
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    38. Viera A, Gómez R, Parra MT, Schmiesing JA, Yokomori K, Rufas JS, Suja JA. Condensin I reveals new insights on mouse meiotic chromosome structure and dynamics. PLoS One. 2007 Aug 22; 2(8):e783. PMID: 17712430; PMCID: PMC1942118.
    39. Kuga T, Nakayama Y, Iwamatsu A, Fukumoto Y, Yokomori K, Yamaguchi N. Separation of a disulfide-linked phosphoprotein by diagonal SDS-PAGE with optimized gel crosslinking. Anal Biochem. 2007 Nov 15; 370(2):252-4. PMID: 17716617.
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    40. Hou F, Chu CW, Kong X, Yokomori K, Zou H. The acetyltransferase activity of San stabilizes the mitotic cohesin at the centromeres in a shugoshin-independent manner. J Cell Biol. 2007 May 21; 177(4):587-97. PMID: 17502424; PMCID: PMC2064205.
    41. Gomez-Godinez V, Wakida NM, Dvornikov AS, Yokomori K, Berns MW. Recruitment of DNA damage recognition and repair pathway proteins following near-IR femtosecond laser irradiation of cells. J Biomed Opt. 2007 Mar-Apr; 12(2):020505. PMID: 17477704.
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    42. Saberi A, Hochegger H, Szuts D, Lan L, Yasui A, Sale JE, Taniguchi Y, Murakawa Y, Zeng W, Yokomori K, Helleday T, Teraoka H, Arakawa H, Buerstedde JM, Takeda S. RAD18 and poly(ADP-ribose) polymerase independently suppress the access of nonhomologous end joining to double-strand breaks and facilitate homologous recombination-mediated repair. Mol Cell Biol. 2007 Apr; 27(7):2562-71. PMID: 17242200; PMCID: PMC1899888.
    43. Kim JS, Heale JT, Zeng W, Kong X, Krasieva TB, Ball AR, Yokomori K. In situ analysis of DNA damage response and repair using laser microirradiation. Methods Cell Biol. 2007; 82:377-407. PMID: 17586265.
      View in: PubMed
    44. Heale JT, Ball AR, Schmiesing JA, Kim JS, Kong X, Zhou S, Hudson DF, Earnshaw WC, Yokomori K. Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. Mol Cell. 2006 Mar 17; 21(6):837-48. PMID: 16543152.
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    45. Kim JS, Krasieva TB, Kurumizaka H, Chen DJ, Taylor AM, Yokomori K. Independent and sequential recruitment of NHEJ and HR factors to DNA damage sites in mammalian cells. J Cell Biol. 2005 Aug 01; 170(3):341-7. PMID: 16061690; PMCID: PMC2171485.
    46. Geiman TM, Sankpal UT, Robertson AK, Chen Y, Mazumdar M, Heale JT, Schmiesing JA, Kim W, Yokomori K, Zhao Y, Robertson KD. Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. Nucleic Acids Res. 2004; 32(9):2716-29. PMID: 15148359; PMCID: PMC419596.
    47. Bermudez VP, Maniwa Y, Tappin I, Ozato K, Yokomori K, Hurwitz J. The alternative Ctf18-Dcc1-Ctf8-replication factor C complex required for sister chromatid cohesion loads proliferating cell nuclear antigen onto DNA. Proc Natl Acad Sci U S A. 2003 Sep 02; 100(18):10237-42. PMID: 12930902; PMCID: PMC193545.
    48. Yokomori K. SMC protein complexes and the maintenance of chromosome integrity. Curr Top Microbiol Immunol. 2003; 274:79-112. PMID: 12596905.
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    49. Kim JS, Krasieva TB, LaMorte V, Taylor AM, Yokomori K. Specific recruitment of human cohesin to laser-induced DNA damage. J Biol Chem. 2002 Nov 22; 277(47):45149-53. PMID: 12228239.
      View in: PubMed
    50. Hakimi MA, Bochar DA, Schmiesing JA, Dong Y, Barak OG, Speicher DW, Yokomori K, Shiekhattar R. A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature. 2002 Aug 29; 418(6901):994-8. PMID: 12198550.
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    51. Ball AR, Schmiesing JA, Zhou C, Gregson HC, Okada Y, Doi T, Yokomori K. Identification of a chromosome-targeting domain in the human condensin subunit CNAP1/hCAP-D2/Eg7. Mol Cell Biol. 2002 Aug; 22(16):5769-81. PMID: 12138188; PMCID: PMC133980.
    52. James RD, Schmiesing JA, Peters AH, Yokomori K, Disteche CM. Differential association of SMC1alpha and SMC3 proteins with meiotic chromosomes in wild-type and SPO11-deficient male mice. Chromosome Res. 2002; 10(7):549-60. PMID: 12498344.
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    53. Gregson HC, Van Hooser AA, Ball AR, Brinkley BR, Yokomori K. Localization of human SMC1 protein at kinetochores. Chromosome Res. 2002; 10(4):267-77. PMID: 12199140.
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