Kyoko Yokomori

Picture of Kyoko Yokomori
Professor, Biological Chemistry
School of Medicine
Graduate Faculty Advisor
Associate Dean for Academic Affairs, Senate
School of Medicine
Ph.D., University of Southern California, 1991, Microbiology
Ph.D., University of Tokyo, Japan, 1995, Veterinary Pathology
D.V.M., Japan, 1988
Phone: (949) 824-8215, 2158
Fax: (949) 824-2688
University of California, Irvine
H129, Hitachi Plumwood
Mail Code: 1700
Irvine, CA 92697
Research Interests
Epigenetics, epigenomics, FSHD, CdLS, cohesin, condensin, SMC complex, DNA damage response and repair, gene regulation, higher-order chromatin organization, chromosome dynamics
Academic Distinctions
1990-1991 Fieger Pre-doctoral Fellowship
1993-1996 Leukemia Society of America Fellow
1996-1999 Leukemia Society of America Special Fellow
1999-2001 March of Dimes Basil O’Connor Starter Scholar Research Award
2000-2005 Leukemia & Lymphoma Society Scholar
1991 – 1992 Postdoctoral Fellow, Dr. Michael Lai's laboratory, Howard Hughes Medical Institute,
University of Southern California, Department of Microbiology
1992 – 1997 Postdoctoral Fellow, Dr. Robert Tjian's laboratory, Howard Hughes Medical Institute,
University of California, Berkeley
Research Abstract
The Yokomori laboratory investigates the mechanisms of chromosome structural organization and how they affect DNA repair and gene regulation in human health and disease. Specifically, we use various DNA damaging methods, including laser microirradiation to study nucleus-wide epigenetic responses to complex DNA damage through PARP signaling and metabolic alteration. The mechanism and function of heterochromatin disruption in FSHD muscular dystrophy is another area of research, in which we perform single cell/nucleus analyses to isolate and characterize a small number of disease-driving cells and are developing 3D and tissue on a chip to measure intrinsic defects of FSHD and CRISPR-engineered mutant myocytes.
Selected publications
(Univ. Tokyo)
1. Yokomori, K., Okada, N., Murai, Y., Goto, N., and Fujiwara, K. (1989). Enterohepatitis in Mongolian gerbils (Meriones unguiculatus) inoculated perorally with Tyzzer's organism (Bacillus piliformis). Laboratory Animal Science 39: 16-20.

(Univ. Southern California)
3. Yokomori, K., La Monica, N., Makino, S., Shieh, C.-K., and Lai, M.M.C. (1989). Biosynthesis, structure and biological activities of envelope protein gp65 of murine coronavirus. Virology 173 : 683-691.

8. Yokomori, K., Baker, S.C., Stohlman, S.A., and Lai, M.M.C. (1992). Hemagglutinin-esterase-specific monoclonal antibodies alter the neuropathogenicity of mouse hepatitis virus. J. Virol. 66 : 2865-2874.

9. Yokomori, K., Banner, L.R., and Lai, M.M.C. (1992). Coronavirus mRNA transcription: UV light transcriptional mapping studies suggest an early requirement for a genomic-length template. J. Virol. 66: 4671-4678.

10. Yokomori, K. and Lai, M. M. C. (1992). Mouse hepatitis virus utilizes two carcinoembryonic antigens as alternative receptors. J. Virol. 66: 6194-6199.

11. Yokomori, K. and Lai, M. M. C. (1992). The receptor for mouse hepatitis virus in the resistant mouse strain SJL is functional: implications for the requirement of a second factor for viral infection. J. Virol. 66: 6931-6938.

17. Chen, D.S., Asanaka, M., Yokomori, K., Wang, F.-I., Hwang, S. B., Li, H.-P., and Lai, M.M.C. (1995). A novel pregnancy-specific glycoprotein is expressed in the brain and serves as a receptor for mouse hepatitis virus. Proc. Natl. Acad. Sci. USA 92: 12095-12099.

(UC Berkeley)
19. Yokomori, K., Admon, A., Goodrich, J.A., Chen, J.-L., and Tjian, R. (1993). Drosophila TFIIA-L is processed into two subunits that are associated with the TBP/TAF complex. Genes & Dev. 7: 2235-2245.

20. Yokomori, K., Chen, J.-L., Admon, A., Zhou, S., and Tjian R. (1993). Molecular cloning and characterization of dTAFII30a and dTAFII30ß: two small subunits of Drosophila TFIID. Genes & Dev. 7: 2587-2597.

21. Verrijzer, C.P., Yokomori, K., Chen, J.-L., and Tjian, R. (1994). Drosophila TAFII150: similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264: 933-941.

22. Yokomori, K., Zeidler, M. P., Chen, J.-L., Verrijzer, C. P., Mlodzik, M., and Tjian, R. (1994). Drosophila TFIIA directs cooperative DNA binding with TBP and mediates transcriptional activation. Genes & Dev. 8: 2313-2323.

23. Chen, J.-L., Attardi, L. D., Verrijzer, C. P., Yokomori, K., and Tjian, R. (1994). Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79: 93-105.

24. Verrijzer, C. P., Chen, J.-L., Yokomori, K., and Tjian, R. (1995). Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81: 1115-1125.

25. Zeidler, M. P., Yokomori, K., Tjian, R., and Mlodzik, M. (1996). Drosophila TFIIA-S is up-regulated and required during Ras-mediated photoreceptor determination. Genes & Dev. 10: 50-59.

26. Yokomori, K., Verrijzer, C.P., and Tjian, R. (1998) An interplay between TBP, TFIIE and TFIIA modulates DNA binding and transcription. Proc. Natl. Acad. Sci. USA 95:6722-27

(UC Irvine)
27. Schmiesing, J.A., Ball, A.R., Gregson, H.C., Alderton, J., Zhou, S. and Yokomori, K. (1998) Identification of two distinct human SMC complexes involved in mitotic chromosome dynamics. Proc. Natl. Acad. Sci. USA 95:12906-11. PMC23650

28. Schmiesing, J. A., Gregson, H. C., Zhou, S., and Yokomori, K. (2000). A human condensin complex containing hCAP-C-hCAP-E and CNAP1, a homolog of Xenopus XCAP-D2, colocalizes with phosphorylated histone H3 during the early stage of mitotic chromosome condensation. Mol. Cell. Biol. 20: 6996-7006.

31. Gregson, H. C., Schmiesing, J. A., Kim, J.-S., Kobayashi, T., Zhou, S., and Yokomori, K. (2001). A potential role for human cohesin in mitotic spindle aster assembly. J. Biol. Chem. 276:47676-47682.

33. Ball, Jr. A. R., Zhou, C., Schmiesing, J. A. Gregson, H. C., Okada, Y., Doi, T., and Yokomori, K. (2002). Identification of a chromosome-targeting domain in the human condensin subunit CNAP1/hCAP-D2/Eg7. Mol. Cell. Biol. 22:5769-5781. PMC133980

34. Hakimi, M.-A., Bochar, D. A., Schmiesing, J. A., Dong, Y., Barak, O. G., Speicher, D. A., Yokomori, K., and Shiekhattar, R. (2002). A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature 418:994-998.

36. Kim, J.-S., Krasieva, T. B., LaMorte, V., Taylor, A. M. R., and Yokomori, K. (2002). Specific recruitment of human cohesin to laser-induced DNA damage. J. Biol. Chem. 277:45149-45153.

38. Bermudez, V. P., Maniwa, Y., Tappin, I., Ozato, K., Yokomori, K., and Hurwitz, J. (2003). 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. 100:10237–10242.

40. Kim, J.-S., Krasieva, T. B., Kurumizaka, H., Chen, D. J., Taylor, A. M. R., and Yokomori, K. (2005). Independent and sequential recruitment of NHEJ and HR factors to DNA damage sites in mammalian cells. J. Cell Biol. 170: 341-7. PMC2171485

41. Heale, J. A., Ball, Jr., A. R., Schmiesing, J. A., Kim, J.-S., Kong, X., Zhou, S., Hudson, D. F., Eanrshaw, W.C., and Yokomori, K. (2006). Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. Molecular Cell 21: 837-48.

44. Hou, F., Chu C. W., Kong, X., Yokomori, K., Zou, H. (2007). The acetyltransferase activity of San stabilizes the mitotic cohesin at the centromeres in a shugoshin-independent manner. J Cell Biol. 177: 587-97.

50. Parelho, V., Hadjur, S.,m Spivakov, M., Leleu, M., Sauer, S., Gregson, H. C., Jarmuz, A., Canzonetta, C., Webster, Z., Nesterova, T., Cobb, B. S., Yokomori, K., Dillon, N., Aragon, L., Fisher, A. G., Merkenschlager, M. (2008). Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132: 422-33.

51. Kong, X., Ball, Jr., A. R., Sonoda, E., Feng, J., Takeda, S., Fukagawa, T., Yen, T. J., and Yokomori, K. (2009). Cohesin associates with spindle poles in a mitosis-specific manner and functions in spindle assembly in vertebrate cells. Mol. Biol. Cell 20: 1289-301. PMC2649254.

52. Kong, X., Mohanty, S., Stephens, J., Heale, J. T., Gomez-Godinez, V., Shi, L., Kim, J.-S., Yokomori, K.* and Berns, M. W.* (2009). Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells. Nucleic Acid Res. 37: e68. (* equal corresponding authors). PMC2685111.

53. Ball, Jr., A. R. and Yokomori, K. (2009). Revisiting the role of Heterochromatin Protein 1 in DNA repair. J. Cell Biol. 185: 573-5.

54. Zeng, W., de Greef, J. C., Chen, Y.-Y., Chien, R., Kong, X., Gregson, H. C., Winokur, S. T., Pyle, A., Robertson, K. D., Schmiesing, J. A., Kimonis, V. E., Balog, J., Frants. R. R., Ball, Jr., A. R., Lock, L. F., Donovan, P. J., van der Maarel, S., and Yokomori, K. (2009). Specific loss of histone H3 lysine 9 trimethylation and HP1?/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 5: e1000559. PMC2700282.

56. Kawauchi, S., Calof, A. L., Santos, R., Lopez-Burks, M. E., Young, C. M., Hoang, M. P., Chua, A., Lao, T., Lechner, M. S., Daniel, J. A., Nussenzweig, A., Kitzes, L., Yokomori, K., Hallgrimsson, B., Lander, A. D. (2009). Multiple Organ System Defects and Transcriptional Dysregulation in the Nipbl+/- Mouse, a Model of Cornelia de Lange Syndrome. PLoS Genet. 5: e1000650. PMC2730539.

57. Yusufzai, T., Kong, X., Yokomori, K., and Kadonaga, J. T. (2009). The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA. Genes Dev. 23: 2000-4. PMC2764493.

58. Zeng, W., Ball, Jr., A. R., and Yokomori, K. (2010). HP1: heterochromatin binding proteins working the genome. Epigenetics 5: 287-92.

60. Wu, S., Wang, W., Kong, X., Congdon1, L. M., Yokomori, K., Kirschner, M. W., and Rice, J. C. (2010). Dynamic regulation of the PR-Set7 histone methyltransferase is required for normal cell cycle progression. Genes Dev. 24: 2531-42. PMC2975929.

61. Chien, R., Zeng, W., Kawauchi, S., Bender, M. A., Santos, R., Gregson, H. C., Schmiesing, J. A., Newkirk, D. A., Kong, X., Ball, Jr., A. R., Calof, A. L., Lander, A. D., Groudine. M., and Yokomori, K. (2011). Cohesin mediates chromatin interactions that regulate mammalian ß-globin expression. J. Biol. Chem. 286: 17870-8. PMC3093862.

62. Ball, Jr., A. R. and Yokomori, K. (2011). Chromatin damage site: open or close? Curr. Opin. Cell Biol. 23: 277-83.

63. Kong, X., Stephens, J. P., Ball, Jr. A. R., Heale, J. T., Newkirk, D. A., Berns, M. W., and Yokomori, K. (2011). Condensin I recruitment to base damage-enriched DNA lesions is modulated by PARP1. PLoS ONE 6: e23548. PMC3155556

64. Chien, R., Zeng, W., Ball, Jr., A. R., and Yokomori, K. (2011). Cohesin: a critical chromatin organizer in mammalian gene regulation. Biochemistry and Cell Biol. 89:445-58.

65. Newkirk, D., Biesinger, J., Chon, A., Yokomori, K., and Xie, X. (2011). AREM: aligning short reads from ChIP-sequencing by expectation maximization. J. Comput. Biol. 18:1495-505. PMC3216101

66. Zeng, W., Ball, Jr., A. R., and Yokomori, K. (2012). The epigenetics of facioscapulohumeral muscular dystrophy. A book chapter in "Epigenomics: From Chromatin Biology to Therapeutics”. Ed. Appasani, K. Cambridge University Press. ISBN: 9781107003828.

68. Wu, N., Kong, X., Ji, Z., Zeng, W., Potts, P. R., Yokomori, K., Yu, H. (2012). Scc1 sumoylation by Mms21 promotes sister chromatid recombination through counteracting Wapl. Genes Dev. 26:1473-85. PMC3403015

70. Ball, Jr. A. R., Chen, Y.-Y., and Yokomori, K. (2014). Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. BBA-Gene Regulatory Mechanisms. 1839: 191-202.

71. Kong, X., Ball, Jr., A. R., Pham, H. X., Zeng, W., Chen, H.-Y., Schmiesing, J. A., Kim, J.-S., Berns, M., and Yokomori, K. (2014). Distinct functions of human cohesin-SA1 and cohesin-SA2 in DNA double-strand break repair. Mol. Cell. Biol. 34: 685-98.

72. Hinde, E., Yokomori, K., Gaus, K., Hahn, K. M., Gratton, E. (2014). Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. Sci. Rep. 4:4219. doi: 10.1038/srep04219.

73. Zeng, W.,* Chen, Y.-Y.,* Newkirk, D. A., Wu, B., Balog, J., Kong, X., Ball, Jr., A. R., Zanotti, S., Tawil, R., Hashimoto, N., Mortazavi, A., van der Maarel, S., and Yokomori, K. (2014). Genetic and epigenetic characteristics of FSHD-associated 4q and 10q D4Z4 that are distinct from non-4q/10q D4Z4 homologs. Hum. Mutat. 35:998-1010. (*co-first authors).

74. Hinde, E.,* Kong, X., Yokomori, K.,* Gratton, E. (2014). Chromatin dynamics during DNA repair revealed by pair correlation analysis of molecular flow in the nucleus. Biophys. J. 107:55-65. (*co-corresponding authors).

75. Tuzon, C. T., Spektor, T., Kong, X., Congdon, L. M., Wu, S., Schotta, G., Yokomori, K., Rice, J. C. (2014). Concerted activities of distinct H4K20 methyltransferases at DNA double-strand breaks regulate 53BP1 nucleation and NHEJ-directed repair Cell Reports 8:430-8. PMC4134327

76. Silva, B. A., Stambaugh, J. R., Yokomori, K.,* Shah, J.I V.*, and Berns, M. W.* (2014). DNA damage to a single chromosome end delays anaphase onset. J. Biol. Chem. 289:22771-84. (*co-corresponding authors).
78. Cruz, G. M. S.,* Kong, X.,* Silva, B. A.,* Khatibzadeh, N., Thai, R., Berns, M. W,§ and Yokomori, K.§ (2016). Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites. Nucleic Acids Res. 44:e27. (*co-first authors; §co-corresponding authors). PMC4756852

79. Zeng, W., Jiang, S., Kong, X., El-Ali, N., Ball, Jr., A. R., Ma, C., I.-H., Hashimoto, H., Yokomori, K.,* and Mortazavi, A.* (2016). Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. Nuc. Acids Res. 44: e158. (*co-corresponding authors). PMC5137429
80. Kong, X., Ball, Jr., A. R., and Yokomori, K. (2017). The use of laser microirradiation to investigate the roles of cohesins in DNA repair. Methods. Mol. Biol. 1515: 227-242. “Cohesin and Condensin: Methods and Protocols”. Editor: Yokomori, K. and Shirahige, K.
81. Newkirk, D. A., Chen, Y.-Y., Chien, R., Zeng, W., Biesinger, J., Flowers, E., Kawauchi, S., Santos, R., Calof, A. L., Lander, A. D., Xie, X.,* and Yokomori, K.* (2017). The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange Syndrome. Clin. Epigenetics 9:89. doi: 10.1186/s13148-017-0391-x. eCollection 2017. (*co-corresponding authors). PMC5574093
83. Kong, X., Cruz, G. M. S., Trinh, S. L., Zhu, X.-D., Berns, M. W.,* and Yokomori, K.* (2018). Biphasic recruitment of TRF2 to DNA damage sites promotes non-sister chromatid homologous recombination repair. J. Cell Science 131(23). pii: jcs219311. doi: 10.1242/jcs.219311. (*co-corresponding authors).
84. Murata, M. M.,§ Kong, X.,§ Moncada, E., Chen, Y., Wang, P., Berns, M. W., Yokomori, K.,* and Digman, M. A.* (2019). NAD consumption by PARP1 in response to DNA damage triggers metabolic shift critical for damaged cell survival. (§ co-first author; * co-corresponding authors). Mol. Biol. Cell 30: 2584-97. PMC6740200.
87. Jiang, S., Williams, K., Kong, X., Zeng, W., Ma, X., Tawil, R., Yokomori, K.,* and Mortazavi, A.* (2020). Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS Genet. 16(5):e1008754. doi: 10.1371/journal.pgen.1008754. (*co-corresponding authors).
88. Chau, J., Kong, X., Nguyen, N., Williams, K., Kiyono, T., Mortazavi, A.,* and Yokomori, K.* (2021). Relationship of DUX4 and target gene expression in FSHD myocytes. Human Mutation (*co-corresponding authors). Selected as Editor’s Choice.
89. Wakida NM, Ha RD, Kim EK, Kong X, Yokomori K, Berns MW. Wakida, N., Ha, R., Kim, E., Kong, X., Yokomori, K., Berns, M. (2021). Nuclear damage signaling and communication in astrocyte networks through PARP-dependent calcium oscillations. Front. Phys. Frontiers in Physics. 2021 April. doi: 10.3389/fphy.2021.598930.
90. Williams K, Yokomori K, Mortazavi A. Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays. Front Genet. 2022;13:835099. doi: 10.3389/fgene.2022.835099. eCollection 2022. Review. PubMed PMID: 35646075; PubMed Central PMCID: PMC9136090.
NIH, FSH Society, NSF
Professional Societies
Other Experience
The Institutional Biosafety Committee Chair
UCI 2007—2011
Graduate Advisor
Dept. Biol. Chem. 2000—pres
SOM Mentoring Committee Chair
Graduate Programs
Cellular and Molecular Biosciences
Mathematical and Computational Biology
Research Centers
CFCCC Cancer Research Institute
Center for Complex Biological Systems
Center for Epigenetics and Metabolism
Developmental Biology Center
Institute for Genomics and Bioinformatics
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