James Kadonaga

Title(s)Professor, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Mechanisms of Eukaryotic Gene Regulation
    NIH R35GM118060May 1, 2016 - Apr 30, 2026
    Role: Principal Investigator
    Elucidation of Human TATA-less Transcription Networks
    NIH R21HG008781Mar 22, 2016 - Dec 31, 2017
    Role: Principal Investigator
    Conference on Chromatin Structure and Activity
    NIH R13CA094873Jan 10, 2002 - Dec 31, 2002
    Role: Principal Investigator
    Chromatin and DNA Dynamics
    NIH R01GM058272Jan 1, 1999 - Jun 30, 2016
    Role: Principal Investigator
    Comprehensive Biology: Exploiting the Yeast Genome
    NIH P41RR011823Sep 30, 1996 - Jun 30, 2016
    Role: Co-Investigator
    NIH R13GM052603Jun 1, 1995 - May 31, 1996
    Role: Principal Investigator
    NIH R01GM046995Jul 1, 1992 - Nov 30, 2004
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Eukaryotes
    NIH R01GM041249Dec 1, 1988 - Nov 30, 2017
    Role: Principal Investigator
    Cell and Molecular Genetics Training Program
    NIH T32GM007240Jul 1, 1975 - Jun 30, 2021
    Role: Principal Investigator

    Collapse Bibliographic 
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    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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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Reconstitution of Chromatin by Stepwise Salt Dialysis. Bio Protoc. 2021 Apr 05; 11(7):e3977. Cruz-Becerra G, Kadonaga JT. PMID: 33889671.
      View in: PubMed   Mentions:
    2. Identification of the human DPR core promoter element using machine learning. Nature. 2020 09; 585(7825):459-463. Vo Ngoc L, Huang CY, Cassidy CJ, Medrano C, Kadonaga JT. PMID: 32908305.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    3. Enhancement of homology-directed repair with chromatin donor templates in cells. Elife. 2020 04 28; 9. Cruz-Becerra G, Kadonaga JT. PMID: 32343230.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    4. The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. Elife. 2019 10 01; 8. Chavez C, Cruz-Becerra G, Fei J, Kassavetis GA, Kadonaga JT. PMID: 31571581.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    5. The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat Struct Mol Biol. 2019 09; 26(9):766-770. Kadonaga JT. PMID: 31439939.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    6. The RNA Polymerase II Core Promoter in Drosophila. Genetics. 2019 05; 212(1):13-24. Vo Ngoc L, Kassavetis GA, Kadonaga JT. PMID: 31053615.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    7. Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS One. 2019; 14(4):e0215695. Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T. PMID: 30998799.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    8. 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. Wang W, Xu J, Limbo O, Fei J, Kassavetis GA, Chong J, Kadonaga JT, Russell P, Li B, Wang D. PMID: 30867290.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    9. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev. 2018 05 01; 32(9-10):682-694. Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. PMID: 29759984.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    10. A simple and versatile system for the ATP-dependent assembly of chromatin. J Biol Chem. 2017 11 24; 292(47):19478-19490. Khuong MT, Fei J, Cruz-Becerra G, Kadonaga JT. PMID: 28982979.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    11. The punctilious RNA polymerase II core promoter. Genes Dev. 2017 07 01; 31(13):1289-1301. Vo Ngoc L, Wang YL, Kassavetis GA, Kadonaga JT. PMID: 28808065.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    12. 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. Vo Ngoc L, Cassidy CJ, Huang CY, Duttke SH, Kadonaga JT. PMID: 28108474.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    13. Prenucleosomes and Active Chromatin. Cold Spring Harb Symp Quant Biol. 2015; 80:65-72. Khuong MT, Fei J, Ishii H, Kadonaga JT. PMID: 26767995.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    14. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev. 2015 Dec 15; 29(24):2563-75. Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT. PMID: 26680301.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    15. Perspectives on Unidirectional versus Divergent Transcription. Mol Cell. 2015 Nov 05; 60(3):348-9. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. PMID: 26545075.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    16. 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. Ishii H, Kadonaga JT, Ren B. PMID: 26080409.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    17. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19; 57(4):674-684. Duttke SHC, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. PMID: 25639469.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    18. 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. 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. PMID: 25512493.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    19. TRF2 and the evolution of the bilateria. Genes Dev. 2014 Oct 01; 28(19):2071-6. Duttke SH, Doolittle RF, Wang YL, Kadonaga JT. PMID: 25274724.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    20. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 2014 Jul 15; 28(14):1550-5. Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. PMID: 24958592.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    21. The annealing helicase and branch migration activities of Drosophila HARP. PLoS One. 2014; 9(5):e98173. Kassavetis GA, Kadonaga JT. PMID: 24866343.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    22. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. Elife. 2013 Aug 20; 2:e00863. Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT. PMID: 23986862.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    23. Biochemical analysis of histone deacetylase-independent transcriptional repression by MeCP2. J Biol Chem. 2013 Mar 08; 288(10):7096-104. Theisen JW, Gucwa JS, Yusufzai T, Khuong MT, Kadonaga JT. PMID: 23349465.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    24. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell. 2013 Jan 17; 152(1-2):120-31. Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E. PMID: 23332750.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    25. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb; 1(1):40-51. Kadonaga JT. PMID: 23801666.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansAnimalsCells
    26. 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. Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT. PMID: 21855802.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    27. Branching out with DNA helicases. Curr Opin Genet Dev. 2011 Apr; 21(2):214-8. Yusufzai T, Kadonaga JT. PMID: 21324673.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    28. 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. Yusufzai T, Kadonaga JT. PMID: 21078962.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    29. 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. Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga JT. PMID: 20801935.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    30. 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. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. PMID: 20683474.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    31. Three key subregions contribute to the function of the downstream RNA polymerase II core promoter. Mol Cell Biol. 2010 Jul; 30(14):3471-9. Theisen JW, Lim CY, Kadonaga JT. PMID: 20457814.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    32. The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA. Genes Dev. 2009 Oct 15; 23(20):2400-4. Yusufzai T, Kong X, Yokomori K, Kadonaga JT. PMID: 19793863.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimalsCells
    33. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol. 2010 Mar 15; 339(2):225-9. Juven-Gershon T, Kadonaga JT. PMID: 19682982.
      View in: PubMed   Mentions: 183     Fields:    Translation:HumansAnimalsCells
    34. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009 Aug; 16(8):847-52. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. PMID: 19620965.
      View in: PubMed   Mentions: 202     Fields:    Translation:AnimalsCells
    35. HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility. Mol Cell. 2009 Jun 12; 34(5):620-6. Rattner BP, Yusufzai T, Kadonaga JT. PMID: 19524541.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    36. HARP is an ATP-driven annealing helicase. Science. 2008 Oct 31; 322(5902):748-50. Yusufzai T, Kadonaga JT. PMID: 18974355.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansCells
    37. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev. 2008 Oct 15; 22(20):2823-30. Juven-Gershon T, Hsu JY, Kadonaga JT. PMID: 18923080.
      View in: PubMed   Mentions: 49     Fields:    Translation:AnimalsCells
    38. 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. Hsu JY, Juven-Gershon T, Marr MT, Wright KJ, Tjian R, Kadonaga JT. PMID: 18703680.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    39. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9715-20. 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. PMID: 18621688.
      View in: PubMed   Mentions: 413     Fields:    Translation:AnimalsCells
    40. The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol. 2008 Jun; 20(3):253-9. Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT. PMID: 18436437.
      View in: PubMed   Mentions: 161     Fields:    Translation:HumansAnimalsCells
    41. CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo. Science. 2007 Aug 24; 317(5841):1087-90. Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga JT, Lusser A, Fyodorov DV. PMID: 17717186.
      View in: PubMed   Mentions: 121     Fields:    Translation:AnimalsCells
    42. Rational design of a super core promoter that enhances gene expression. Nat Methods. 2006 Nov; 3(11):917-22. Juven-Gershon T, Cheng S, Kadonaga JT. PMID: 17124735.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimalsCells
    43. 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. Santoso B, Kadonaga JT. PMID: 16415879.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    44. 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. Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen'ev MB, Kadonaga JT, Georgieva SG, Tora L. PMID: 16330756.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    45. 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. Gemmen GJ, Sim R, Haushalter KA, Ke PC, Kadonaga JT, Smith DE. PMID: 16002089.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    46. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat Struct Mol Biol. 2005 Feb; 12(2):160-6. Lusser A, Urwin DL, Kadonaga JT. PMID: 15643425.
      View in: PubMed   Mentions: 137     Fields:    Translation:AnimalsCells
    47. Strategies for the reconstitution of chromatin. Nat Methods. 2004 Oct; 1(1):19-26. Lusser A, Kadonaga JT. PMID: 15789029.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    48. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 2004 Jul 01; 18(13):1606-17. Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT. PMID: 15231738.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansCells
    49. 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. Alexiadis V, Lusser A, Kadonaga JT. PMID: 15105430.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    50. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell. 2004 Jan 23; 116(2):247-57. Kadonaga JT. PMID: 14744435.
      View in: PubMed   Mentions: 149     Fields:    Translation:HumansAnimalsCells
    51. 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. Fyodorov DV, Blower MD, Karpen GH, Kadonaga JT. PMID: 14752009.
      View in: PubMed   Mentions: 84     Fields:    Translation:AnimalsCells
    52. Chromatin remodeling by ATP-dependent molecular machines. Bioessays. 2003 Dec; 25(12):1192-200. Lusser A, Kadonaga JT. PMID: 14635254.
      View in: PubMed   Mentions: 101     Fields:    Translation:AnimalsCells
    53. Chromatin assembly by DNA-translocating motors. Nat Rev Mol Cell Biol. 2003 Aug; 4(8):613-20. Haushalter KA, Kadonaga JT. PMID: 12923523.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    54. The RNA polymerase II core promoter. Annu Rev Biochem. 2003; 72:449-79. Smale ST, Kadonaga JT. PMID: 12651739.
      View in: PubMed   Mentions: 394     Fields:    Translation:HumansAnimalsCells
    55. Histone deacetylation by Sir2 generates a transcriptionally repressed nucleoprotein complex. Proc Natl Acad Sci U S A. 2003 Feb 18; 100(4):1609-14. Parsons XH, Garcia SN, Pillus L, Kadonaga JT. PMID: 12571358.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    56. Chromatin assembly in vitro with purified recombinant ACF and NAP-1. Methods Enzymol. 2003; 371:499-515. Fyodorov DV, Kadonaga JT. PMID: 14712724.
      View in: PubMed   Mentions: 46     Fields:    Translation:AnimalsCells
    57. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 2002 Nov 01; 16(21):2767-71. Alexiadis V, Kadonaga JT. PMID: 12414729.
      View in: PubMed   Mentions: 64     Fields:    Translation:AnimalsCells
    58. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 2002 Oct 15; 16(20):2583-92. Butler JE, Kadonaga JT. PMID: 12381658.
      View in: PubMed   Mentions: 204     Fields:    Translation:HumansAnimalsCells
    59. The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med. 2002 Sep 30; 34(4):259-64. Kadonaga JT. PMID: 12515390.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    60. 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. Fyodorov DV, Kadonaga JT. PMID: 12192034.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    61. Dynamics of ATP-dependent chromatin assembly by ACF. Nature. 2002 Aug 22; 418(6900):897-900. Fyodorov DV, Kadonaga JT. PMID: 12192415.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    62. Biochemical analysis of chromatin containing recombinant Drosophila core histones. J Biol Chem. 2002 Mar 08; 277(10):8749-54. Levenstein ME, Kadonaga JT. PMID: 11773058.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
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