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James Kadonaga

Title(s)Researcher, Molecular Biology
SchoolAcademic Aff
Phone858-534-4608
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    Collapse Research 
    Collapse Research Activities and Funding
    Mechanisms of Eukaryotic Gene Regulation
    NIH/NIGMS R35GM118060May 1, 2016 - Apr 30, 2021
    Role: Principal Investigator
    Elucidation of Human TATA-less Transcription Networks
    NIH/NHGRI R21HG008781Mar 22, 2016 - Dec 31, 2017
    Role: Principal Investigator
    Conference on Chromatin Structure and Activity
    NIH/NCI R13CA094873Jan 10, 2002 - Dec 31, 2002
    Role: Principal Investigator
    Chromatin and DNA Dynamics
    NIH/NIGMS R01GM058272Jan 1, 1999 - Jun 30, 2019
    Role: Principal Investigator
    Comprehensive Biology: Exploiting the Yeast Genome
    NIH P41RR011823Sep 30, 1996 - Jun 30, 2016
    Role: Co-Investigator
    FASEB RESEARCH CONFERENCE--CHROMATIN AND TRANSCRIPTION
    NIH/NIGMS R13GM052603Jun 1, 1995 - May 31, 1996
    Role: Principal Investigator
    CHROMATIN STRUCTURE AND GENE ACTIVITY
    NIH/NIGMS R01GM046995Jul 1, 1992 - Nov 30, 2004
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Eukaryotes
    NIH/NIGMS R01GM041249Dec 1, 1988 - Nov 30, 2017
    Role: Principal Investigator
    Cell and Molecular Genetics Training Program
    NIH/NIGMS T32GM007240Jul 1, 1975 - Jun 30, 2020
    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.
    List All   |   Timeline
    1. Kadonaga JT. The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat Struct Mol Biol. 2019 Aug 22. PMID: 31439939.
      View in: PubMed
    2. Vo Ngoc L, Kassavetis GA, Kadonaga JT. The RNA Polymerase II Core Promoter in Drosophila. Genetics. 2019 05; 212(1):13-24. PMID: 31053615.
      View in: PubMed
    3. Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T. Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS One. 2019; 14(4):e0215695. PMID: 30998799.
      View in: PubMed
    4. Wang W, Xu J, Limbo O, Fei J, Kassavetis GA, Chong J, Kadonaga JT, Russell P, Li B, Wang D. Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog. Proc Natl Acad Sci U S A. 2019 03 26; 116(13):6120-6129. PMID: 30867290.
      View in: PubMed
    5. Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev. 2018 05 01; 32(9-10):682-694. PMID: 29759984.
      View in: PubMed
    6. Khuong MT, Fei J, Cruz-Becerra G, Kadonaga JT. A simple and versatile system for the ATP-dependent assembly of chromatin. J Biol Chem. 2017 11 24; 292(47):19478-19490. PMID: 28982979.
      View in: PubMed
    7. Vo Ngoc L, Wang YL, Kassavetis GA, Kadonaga JT. The punctilious RNA polymerase II core promoter. Genes Dev. 2017 07 01; 31(13):1289-1301. PMID: 28808065.
      View in: PubMed
    8. Vo Ngoc L, Cassidy CJ, Huang CY, Duttke SH, Kadonaga JT. The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. Genes Dev. 2017 01 01; 31(1):6-11. PMID: 28108474.
      View in: PubMed
    9. Khuong MT, Fei J, Ishii H, Kadonaga JT. Prenucleosomes and Active Chromatin. Cold Spring Harb Symp Quant Biol. 2015; 80:65-72. PMID: 26767995.
      View in: PubMed
    10. Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev. 2015 Dec 15; 29(24):2563-75. PMID: 26680301; PMCID: PMC4699385.
    11. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Perspectives on Unidirectional versus Divergent Transcription. Mol Cell. 2015 Nov 05; 60(3):348-9. PMID: 26545075; PMCID: PMC4643650 [Available on 11/05/16].
    12. Ishii H, Kadonaga JT, Ren B. MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A. 2015 Jul 07; 112(27):E3457-65. PMID: 26080409; PMCID: PMC4500276.
    13. Duttke SHC, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19; 57(4):674-684. PMID: 25639469.
      View in: PubMed
    14. Wang L, Limbo O, Fei J, Chen L, Kim B, Luo J, Chong J, Conaway RC, Conaway JW, Ranish JA, Kadonaga JT, Russell P, Wang D. Regulation of the Rhp26ERCC6/CSB chromatin remodeler by a novel conserved leucine latch motif. Proc Natl Acad Sci U S A. 2014 Dec 30; 111(52):18566-71. PMID: 25512493; PMCID: PMC4284531.
    15. Duttke SH, Doolittle RF, Wang YL, Kadonaga JT. TRF2 and the evolution of the bilateria. Genes Dev. 2014 Oct 01; 28(19):2071-6. PMID: 25274724; PMCID: PMC4180970.
    16. Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 2014 Jul 15; 28(14):1550-5. PMID: 24958592; PMCID: PMC4102762.
    17. Kassavetis GA, Kadonaga JT. The annealing helicase and branch migration activities of Drosophila HARP. PLoS One. 2014; 9(5):e98173. PMID: 24866343; PMCID: PMC4035279.
    18. Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. Elife. 2013 Aug 20; 2:e00863. PMID: 23986862; PMCID: PMC3748710.
    19. Theisen JW, Gucwa JS, Yusufzai T, Khuong MT, Kadonaga JT. Biochemical analysis of histone deacetylase-independent transcriptional repression by MeCP2. J Biol Chem. 2013 Mar 08; 288(10):7096-104. PMID: 23349465; PMCID: PMC3591619.
    20. Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell. 2013 Jan 17; 152(1-2):120-31. PMID: 23332750; PMCID: PMC3552382.
    21. Kadonaga JT. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb; 1(1):40-51. PMID: 23801666; PMCID: PMC3695423.
    22. Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT. Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF. Mol Cell. 2011 Aug 19; 43(4):638-48. PMID: 21855802; PMCID: PMC3160715.
    23. Yusufzai T, Kadonaga JT. Branching out with DNA helicases. Curr Opin Genet Dev. 2011 Apr; 21(2):214-8. PMID: 21324673; PMCID: PMC3079503.
    24. Yusufzai T, Kadonaga JT. Annealing helicase 2 (AH2), a DNA-rewinding motor with an HNH motif. Proc Natl Acad Sci U S A. 2010 Dec 07; 107(49):20970-3. PMID: 21078962; PMCID: PMC3000258.
    25. Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga JT. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev. 2010 Sep 15; 24(18):2013-8. PMID: 20801935; PMCID: PMC2939363.
    26. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.". Nat Struct Mol Biol. 2010 Aug; 17(8):920-3. PMID: 20683474; PMCID: PMC4742340.
    27. Theisen JW, Lim CY, Kadonaga JT. Three key subregions contribute to the function of the downstream RNA polymerase II core promoter. Mol Cell Biol. 2010 Jul; 30(14):3471-9. PMID: 20457814; PMCID: PMC2897566.
    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. Juven-Gershon T, Kadonaga JT. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol. 2010 Mar 15; 339(2):225-9. PMID: 19682982; PMCID: PMC2830304.
    30. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009 Aug; 16(8):847-52. PMID: 19620965; PMCID: PMC2823114.
    31. Rattner BP, Yusufzai T, Kadonaga JT. HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility. Mol Cell. 2009 Jun 12; 34(5):620-6. PMID: 19524541; PMCID: PMC2709789.
    32. Yusufzai T, Kadonaga JT. HARP is an ATP-driven annealing helicase. Science. 2008 Oct 31; 322(5902):748-50. PMID: 18974355; PMCID: PMC2587503.
    33. Juven-Gershon T, Hsu JY, Kadonaga JT. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev. 2008 Oct 15; 22(20):2823-30. PMID: 18923080; PMCID: PMC2569877.
    34. Hsu JY, Juven-Gershon T, Marr MT, Wright KJ, Tjian R, Kadonaga JT. TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes Dev. 2008 Sep 01; 22(17):2353-8. PMID: 18703680; PMCID: PMC2532932.
    35. Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9715-20. PMID: 18621688; PMCID: PMC2447866.
    36. Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT. The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol. 2008 Jun; 20(3):253-9. PMID: 18436437; PMCID: PMC2586601.
    37. Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga JT, Lusser A, Fyodorov DV. CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo. Science. 2007 Aug 24; 317(5841):1087-90. PMID: 17717186; PMCID: PMC3014568.
    38. Juven-Gershon T, Cheng S, Kadonaga JT. Rational design of a super core promoter that enhances gene expression. Nat Methods. 2006 Nov; 3(11):917-22. PMID: 17124735.
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    39. Santoso B, Kadonaga JT. Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300. Nat Struct Mol Biol. 2006 Feb; 13(2):131-9. PMID: 16415879.
      View in: PubMed
    40. Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen'ev MB, Kadonaga JT, Georgieva SG, Tora L. Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation. Proc Natl Acad Sci U S A. 2005 Dec 13; 102(50):18087-92. PMID: 16330756; PMCID: PMC1306797.
    41. Gemmen GJ, Sim R, Haushalter KA, Ke PC, Kadonaga JT, Smith DE. Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF. J Mol Biol. 2005 Aug 05; 351(1):89-99. PMID: 16002089.
      View in: PubMed
    42. Lusser A, Urwin DL, Kadonaga JT. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat Struct Mol Biol. 2005 Feb; 12(2):160-6. PMID: 15643425.
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    43. Lusser A, Kadonaga JT. Strategies for the reconstitution of chromatin. Nat Methods. 2004 Oct; 1(1):19-26. PMID: 15789029.
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    44. Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 2004 Jul 01; 18(13):1606-17. PMID: 15231738; PMCID: PMC443522.
    45. Alexiadis V, Lusser A, Kadonaga JT. A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing. J Biol Chem. 2004 Jun 25; 279(26):27824-9. PMID: 15105430.
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    46. Kadonaga JT. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell. 2004 Jan 23; 116(2):247-57. PMID: 14744435.
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    47. Fyodorov DV, Blower MD, Karpen GH, Kadonaga JT. Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 2004 Jan 15; 18(2):170-83. PMID: 14752009.
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    48. Lusser A, Kadonaga JT. Chromatin remodeling by ATP-dependent molecular machines. Bioessays. 2003 Dec; 25(12):1192-200. PMID: 14635254.
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    49. Haushalter KA, Kadonaga JT. Chromatin assembly by DNA-translocating motors. Nat Rev Mol Cell Biol. 2003 Aug; 4(8):613-20. PMID: 12923523.
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    50. Smale ST, Kadonaga JT. The RNA polymerase II core promoter. Annu Rev Biochem. 2003; 72:449-79. PMID: 12651739.
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    51. Parsons XH, Garcia SN, Pillus L, Kadonaga JT. Histone deacetylation by Sir2 generates a transcriptionally repressed nucleoprotein complex. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1609-14. PMID: 12571358; PMCID: PMC149880.
    52. Fyodorov DV, Kadonaga JT. Chromatin assembly in vitro with purified recombinant ACF and NAP-1. Methods Enzymol. 2003; 371:499-515. PMID: 14712724.
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    53. Alexiadis V, Kadonaga JT. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 2002 Nov 01; 16(21):2767-71. PMID: 12414729; PMCID: PMC187467.
    54. Butler JE, Kadonaga JT. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 2002 Oct 15; 16(20):2583-92. PMID: 12381658.
      View in: PubMed
    55. Kadonaga JT. The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med. 2002 Sep 30; 34(4):259-64. PMID: 12515390.
      View in: PubMed
    56. Fyodorov DV, Kadonaga JT. Binding of Acf1 to DNA involves a WAC motif and is important for ACF-mediated chromatin assembly. Mol Cell Biol. 2002 Sep; 22(18):6344-53. PMID: 12192034; PMCID: PMC135643.
    57. Fyodorov DV, Kadonaga JT. Dynamics of ATP-dependent chromatin assembly by ACF. Nature. 2002 Aug 22; 418(6900):897-900. PMID: 12192415.
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    58. Levenstein ME, Kadonaga JT. Biochemical analysis of chromatin containing recombinant Drosophila core histones. J Biol Chem. 2002 Mar 08; 277(10):8749-54. PMID: 11773058.
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