Huilin Zhou

Title(s)Professor, Cellular and Molecular Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Gross chromosomal rearrangements (GCRs), including chromosomal translocations, inversions and other rearrangements, are a hallmark of human cancers. The goal of my laboratory is to study the specific signaling pathways, utilizing phosphorylation, sumoylation and ubiquitination that act to maintain genome integrity. We chose Saccharomyces cerevisiae as a model system due to its available genetic assays and because it allows facile biochemical and proteomic studies. Studies in my laboratory have focused on two areas: 1) the DNA damage checkpoint, and 2) protein sumoylation and ubiquitination in genome maintenance. A convergence of genetic, biochemical and proteomic approaches are being pursued to study the molecular mechanisms of signaling pathways that specifically prevent genome rearrangements.

    Research Focus Areas:

  • Biochemistry and Structural Biology

  • Cell Division and Cell Cycle Control

  • DNA Replication and Repair

  • Genetics and Genomics

  • Signal Transduction


    • Collapse Research 
    Collapse research activities and funding
    Orbitrap Fusion Mass Spectrometer
    NIH S10OD023498Mar 15, 2017 - Mar 14, 2018
    Role: Principal Investigator
    Suppression of duplication-mediated genome rearrangements by protein sumoylation
    NIH R01GM116897Sep 30, 2015 - Mar 31, 2024
    Role: Principal Investigator
    Regulation and functions of DNA damage checkpoint kinases in Yeast
    NIH R01GM080469Apr 1, 2007 - Mar 31, 2014
    Role: Principal Investigator
    Technology for the Analysis of Protein Phosphorylation
    NIH K22HG002604Sep 30, 2002 - Aug 31, 2006
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected 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. to make corrections and additions.
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    1. Sequence specificity of an essential nuclear localization sequence in Mcm3. PLoS Genet. 2025 Jan; 21(1):e1011499. Wang Z, Zhang YJ, Zhang QY, Bilsborrow K, Leslie M, Suhandynata RT, Zhou H. PMID: 39836669; PMCID: PMC11761085.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Concatemer-assisted stoichiometry analysis: targeted mass spectrometry for protein quantification. Life Sci Alliance. 2025 Mar; 8(3). Cai J, Quan Y, Zhang CY, Wang Z, Hinshaw SM, Zhou H, Suhandynata RT. PMID: 39741008; PMCID: PMC11707388.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    3. Sequence specificity of an essential nuclear localization sequence in Mcm3. bioRxiv. 2024 Nov 14. Wang Z, Zhang YJ, Zhang QY, Bilsborrow K, Leslie M, Suhandynata RT, Zhou H. PMID: 39605614; PMCID: PMC11601334.
      View in: PubMed   Mentions:
    4. Concatemer Assisted Stoichiometry Analysis (CASA): targeted mass spectrometry for protein quantification. bioRxiv. 2024 Jul 27. Cai J, Yun Q, Zhang CY, Wang Z, Hinshaw SM, Zhou H, Suhandynata RT. PMID: 39091769; PMCID: PMC11291133.
      View in: PubMed   Mentions:
    5. A eukaryotic-like ubiquitination system in bacterial antiviral defence. Nature. 2024 Jul; 631(8022):843-849. Chambers LR, Ye Q, Cai J, Gong M, Ledvina HE, Zhou H, Whiteley AT, Suhandynata RT, Corbett KD. PMID: 39020180; PMCID: PMC11476048.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    6. Bacterial antiviral defense pathways encode eukaryotic-like ubiquitination systems. bioRxiv. 2023 Sep 26. Chambers LR, Ye Q, Cai J, Gong M, Ledvina HE, Zhou H, Whiteley AT, Suhandynata RT, Corbett KD. PMID: 37808811; PMCID: PMC10557695.
      View in: PubMed   Mentions:
    7. The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. Mol Cell. 2022 11 03; 82(21):4145-4159.e7. Deep A, Gu Y, Gao YQ, Ego KM, Herzik MA, Zhou H, Corbett KD. PMID: 36206765; PMCID: PMC9637719.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    8. Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB. EMBO J. 2022 09 01; 41(17):e110698. Li FL, Wu Z, Gao YQ, Bowling FZ, Franklin JM, Hu C, Suhandynata RT, Frohman MA, Airola MV, Zhou H, Guan KL. PMID: 35844135; PMCID: PMC9433938.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    9. Site-specific MCM sumoylation prevents genome rearrangements by controlling origin-bound MCM. PLoS Genet. 2022 06; 18(6):e1010275. Quan Y, Zhang QY, Zhou AL, Wang Y, Cai J, Gao YQ, Zhou H. PMID: 35696436; PMCID: PMC9232163.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    10. Ctf3/CENP-I provides a docking site for the desumoylase Ulp2 at the kinetochore. J Cell Biol. 2021 08 02; 220(8). Quan Y, Hinshaw SM, Wang PC, Harrison SC, Zhou H. PMID: 34081091; PMCID: PMC8178754.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    11. Shared and distinct roles of Esc2 and Mms21 in suppressing genome rearrangements and regulating intracellular sumoylation. PLoS One. 2021; 16(2):e0247132. Suhandynata RT, Gao YQ, Zhou AL, Yang Y, Wang PC, Zhou H. PMID: 33600463; PMCID: PMC7891725.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    12. Recruitment of the Ulp2 protease to the inner kinetochore prevents its hyper-sumoylation to ensure accurate chromosome segregation. PLoS Genet. 2019 11; 15(11):e1008477. Suhandynata RT, Quan Y, Yang Y, Yuan WT, Albuquerque CP, Zhou H. PMID: 31747400; PMCID: PMC6892545.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    13. Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma Radiation Sensitivity through Attenuated DNA Repair. Cancer Cell. 2019 03 18; 35(3):504-518.e7. Ma J, Benitez JA, Li J, Miki S, Ponte de Albuquerque C, Galatro T, Orellana L, Zanca C, Reed R, Boyer A, Koga T, Varki NM, Fenton TR, Nagahashi Marie SK, Lindahl E, Gahman TC, Shiau AK, Zhou H, DeGroot J, Sulman EP, Cavenee WK, Kolodner RD, Chen CC, Furnari FB. PMID: 30827889; PMCID: PMC6424615.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    14. Binding to small ubiquitin-like modifier and the nucleolar protein Csm1 regulates substrate specificity of the Ulp2 protease. J Biol Chem. 2018 08 03; 293(31):12105-12119. de Albuquerque CP, Suhandynata RT, Carlson CR, Yuan WT, Zhou H. PMID: 29903909; PMCID: PMC6078457.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    15. SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements. PLoS Genet. 2018 03; 14(3):e1007250. Liang J, Li BZ, Tan AP, Kolodner RD, Putnam CD, Zhou H. PMID: 29505562; PMCID: PMC5860785.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    16. mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT. Mol Cell. 2017 Jul 06; 67(1):128-138.e7. Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS. PMID: 28648777; PMCID: PMC5521991.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansCells
    17. A Chemical and Enzymatic Approach to Study Site-Specific Sumoylation. PLoS One. 2015; 10(12):e0143810. Albuquerque CP, Yeung E, Ma S, Fu T, Corbett KD, Zhou H. PMID: 26633173; PMCID: PMC4669148.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    18. Proteomics studies of the interactome of RNA polymerase II C-terminal repeated domain. BMC Res Notes. 2015 Oct 29; 8:616. Pineda G, Shen Z, de Albuquerque CP, Reynoso E, Chen J, Tu CC, Tang W, Briggs S, Zhou H, Wang JY. PMID: 26515650; PMCID: PMC4627417.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    19. Trends in urodynamics study utilization in a Southern California managed care population. Am J Obstet Gynecol. 2015 Nov; 213(5):724.e1-6. Lippmann QK, Diwadkar GB, Zhou H, Menefee SA. PMID: 26164690.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    20. ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP. Nat Commun. 2015 Jan 27; 6:6171. Sun S, Ling SC, Qiu J, Albuquerque CP, Zhou Y, Tokunaga S, Li H, Qiu H, Bui A, Yeo GW, Huang EJ, Eggan K, Zhou H, Fu XD, Lagier-Tourenne C, Cleveland DW. PMID: 25625564; PMCID: PMC4338613.
      View in: PubMed   Mentions: 126     Fields:    
    21. Both decreased and increased SRPK1 levels promote cancer by interfering with PHLPP-mediated dephosphorylation of Akt. Mol Cell. 2014 May 08; 54(3):378-91. Wang P, Zhou Z, Hu A, Ponte de Albuquerque C, Zhou Y, Hong L, Sierecki E, Ajiro M, Kruhlak M, Harris C, Guan KL, Zheng ZM, Newton AC, Sun P, Zhou H, Fu XD. PMID: 24703948; PMCID: PMC4019712.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
    22. DNA damage triggers Golgi dispersal via DNA-PK and GOLPH3. Cell. 2014 Jan 30; 156(3):413-27. Farber-Katz SE, Dippold HC, Buschman MD, Peterman MC, Xing M, Noakes CJ, Tat J, Ng MM, Rahajeng J, Cowan DM, Fuchs GJ, Zhou H, Field SJ. PMID: 24485452; PMCID: PMC4018323.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimalsCells
    23. Distinct SUMO ligases cooperate with Esc2 and Slx5 to suppress duplication-mediated genome rearrangements. PLoS Genet. 2013; 9(8):e1003670. Albuquerque CP, Wang G, Lee NS, Kolodner RD, Putnam CD, Zhou H. PMID: 23935535; PMCID: PMC3731205.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    24. The co-repressor SMRT delays DNA damage-induced caspase activation by repressing pro-apoptotic genes and modulating the dynamics of checkpoint kinase 2 activation. PLoS One. 2013; 8(5):e59986. Scafoglio C, Smolka M, Zhou H, Perissi V, Rosenfeld MG. PMID: 23690919; PMCID: PMC3656868.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    25. Direct binding of SAS-6 to ZYG-1 recruits SAS-6 to the mother centriole for cartwheel assembly. Dev Cell. 2013 May 13; 25(3):284-98. Lettman MM, Wong YL, Viscardi V, Niessen S, Chen SH, Shiau AK, Zhou H, Desai A, Oegema K. PMID: 23673331; PMCID: PMC3655416.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    26. Preserving Yeast Genetic Heritage through DNA Damage Checkpoint Regulation and Telomere Maintenance. Biomolecules. 2012 Oct 30; 2(4):505-23. Baldo V, Liang J, Wang G, Zhou H. PMID: 24970147; PMCID: PMC4030855.
      View in: PubMed   Mentions: 3     Fields:    
    27. Multiple phosphorylation of Rad9 by CDK is required for DNA damage checkpoint activation. Cell Cycle. 2012 Oct 15; 11(20):3792-800. Wang G, Tong X, Weng S, Zhou H. PMID: 23070520; PMCID: PMC3495822.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    28. Resistance to EGF receptor inhibitors in glioblastoma mediated by phosphorylation of the PTEN tumor suppressor at tyrosine 240. Proc Natl Acad Sci U S A. 2012 Aug 28; 109(35):14164-9. Fenton TR, Nathanson D, Ponte de Albuquerque C, Kuga D, Iwanami A, Dang J, Yang H, Tanaka K, Oba-Shinjo SM, Uno M, Inda MM, Wykosky J, Bachoo RM, James CD, DePinho RA, Vandenberg SR, Zhou H, Marie SK, Mischel PS, Cavenee WK, Furnari FB. PMID: 22891331; PMCID: PMC3435194.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    29. Quantitative phosphoproteomics: New technologies and applications in the DNA damage response. Cell Cycle. 2010 Sep 01; 9(17):3479-84. Zhou H, Albuquerque CP, Liang J, Suhandynata RT, Weng S. PMID: 20855976; PMCID: PMC3230475.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    30. ALS-associated mutations in TDP-43 increase its stability and promote TDP-43 complexes with FUS/TLS. Proc Natl Acad Sci U S A. 2010 Jul 27; 107(30):13318-23. Ling SC, Albuquerque CP, Han JS, Lagier-Tourenne C, Tokunaga S, Zhou H, Cleveland DW. PMID: 20624952; PMCID: PMC2922163.
      View in: PubMed   Mentions: 205     Fields:    Translation:HumansCells
    31. A proteome-wide analysis of kinase-substrate network in the DNA damage response. J Biol Chem. 2010 Apr 23; 285(17):12803-12. Chen SH, Albuquerque CP, Liang J, Suhandynata RT, Zhou H. PMID: 20190278; PMCID: PMC2857137.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    32. GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch and shape the Golgi to promote budding. Cell. 2009 Oct 16; 139(2):337-51. Dippold HC, Ng MM, Farber-Katz SE, Lee SK, Kerr ML, Peterman MC, Sim R, Wiharto PA, Galbraith KA, Madhavarapu S, Fuchs GJ, Meerloo T, Farquhar MG, Zhou H, Field SJ. PMID: 19837035; PMCID: PMC2779841.
      View in: PubMed   Mentions: 211     Fields:    
    33. Reconstitution of Rad53 activation by Mec1 through adaptor protein Mrc1. J Biol Chem. 2009 Jul 10; 284(28):18593-604. Chen SH, Zhou H. PMID: 19457865; PMCID: PMC2707194.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    34. Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS One. 2009; 4(1):e4300. Wagner MV, Smolka MB, de Bruin RA, Zhou H, Wittenberg C, Dowdy SF. PMID: 19172996; PMCID: PMC2627923.
      View in: PubMed   Mentions: 40     Fields:    
    35. hNOA1 interacts with complex I and DAP3 and regulates mitochondrial respiration and apoptosis. J Biol Chem. 2009 Feb 20; 284(8):5414-24. Tang T, Zheng B, Chen SH, Murphy AN, Kudlicka K, Zhou H, Farquhar MG. PMID: 19103604; PMCID: PMC2643507.
      View in: PubMed   Mentions: 24     Fields:    
    36. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res. 2008 Aug; 7(8):3373-81. Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. PMID: 18563926; PMCID: PMC2566938.
      View in: PubMed   Mentions: 24     Fields:    
    37. The endocytic adaptor protein ARH associates with motor and centrosomal proteins and is involved in centrosome assembly and cytokinesis. Mol Biol Cell. 2008 Jul; 19(7):2949-61. Lehtonen S, Shah M, Nielsen R, Iino N, Ryan JJ, Zhou H, Farquhar MG. PMID: 18417616; PMCID: PMC2441659.
      View in: PubMed   Mentions: 20     Fields:    
    38. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics. 2008 Jul; 7(7):1389-96. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. PMID: 18407956; PMCID: PMC2493382.
      View in: PubMed   Mentions: 254     Fields:    
    39. An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension. Hum Mol Genet. 2007 Jul 15; 16(14):1752-64. Wen G, Wessel J, Zhou W, Ehret GB, Rao F, Stridsberg M, Mahata SK, Gent PM, Das M, Cooper RS, Chakravarti A, Zhou H, Schork NJ, O'connor DT, Hamilton BA. PMID: 17584765; PMCID: PMC2695823.
      View in: PubMed   Mentions: 12     Fields:    
    40. An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol. 2006 Dec 04; 175(5):743-53. Smolka MB, Chen SH, Maddox PS, Enserink JM, Albuquerque CP, Wei XX, Desai A, Kolodner RD, Zhou H. PMID: 17130285; PMCID: PMC2064674.
      View in: PubMed   Mentions: 51     Fields:    
    41. Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol. 2006 Dec 04; 175(5):729-41. Enserink JM, Smolka MB, Zhou H, Kolodner RD. PMID: 17130284; PMCID: PMC2064673.
      View in: PubMed   Mentions: 41     Fields:    
    42. Mechanism of Dun1 activation by Rad53 phosphorylation in Saccharomyces cerevisiae. J Biol Chem. 2007 Jan 12; 282(2):986-95. Chen SH, Smolka MB, Zhou H. PMID: 17114794; PMCID: PMC2811688.
      View in: PubMed   Mentions: 39     Fields:    
    43. Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants. Proc Natl Acad Sci U S A. 2006 Mar 07; 103(10):3710-5. Kats ES, Albuquerque CP, Zhou H, Kolodner RD. PMID: 16501045; PMCID: PMC1533778.
      View in: PubMed   Mentions: 16     Fields:    
    44. Mass spectrometric and kinetic analysis of ASF/SF2 phosphorylation by SRPK1 and Clk/Sty. J Biol Chem. 2005 Dec 16; 280(50):41761-8. Velazquez-Dones A, Hagopian JC, Ma CT, Zhong XY, Zhou H, Ghosh G, Fu XD, Adams JA. PMID: 16223727.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    45. Tandem mass spectrometry identifies proteins phosphorylated by cyclic AMP-dependent protein kinase when sea urchin sperm undergo the acrosome reaction. Dev Biol. 2005 Sep 01; 285(1):116-25. Su YH, Chen SH, Zhou H, Vacquier VD. PMID: 16038896.
      View in: PubMed   Mentions: 5     Fields:    
    46. Cell junction-associated proteins IQGAP1, MAGI-2, CASK, spectrins, and alpha-actinin are components of the nephrin multiprotein complex. Proc Natl Acad Sci U S A. 2005 Jul 12; 102(28):9814-9. Lehtonen S, Ryan JJ, Kudlicka K, Iino N, Zhou H, Farquhar MG. PMID: 15994232; PMCID: PMC1175008.
      View in: PubMed   Mentions: 63     Fields:    Translation:AnimalsCells
    47. Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag. Mol Cell Proteomics. 2005 Sep; 4(9):1358-69. Smolka MB, Albuquerque CP, Chen SH, Schmidt KH, Wei XX, Kolodner RD, Zhou H. PMID: 15972895; PMCID: PMC2813687.
      View in: PubMed   Mentions: 33     Fields:    
    48. Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton. EMBO J. 2004 Oct 01; 23(19):3747-57. Audhya A, Loewith R, Parsons AB, Gao L, Tabuchi M, Zhou H, Boone C, Hall MN, Emr SD. PMID: 15372071; PMCID: PMC522789.
      View in: PubMed   Mentions: 64     Fields:    
    49. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J Biol Chem. 2004 Jul 30; 279(31):32262-8. Zhou W, Ryan JJ, Zhou H. PMID: 15166219; PMCID: PMC2810850.
      View in: PubMed   Mentions: 128     Fields:    
    50. Quantitative protein analysis by solid phase isotope tagging and mass spectrometry. Methods Mol Biol. 2004; 261:511-8. Zhou H, Boyle R, Aebersold R. PMID: 15064479.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
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