James Kadonaga

Title(s)Professor, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
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    Mechanisms of Eukaryotic Gene Regulation
    NIH R35GM118060May 1, 2016 - Apr 30, 2021
    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 - Dec 31, 2014
    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 - Dec 14, 1996
    Role: Principal Investigator
    Mechanisms of Transcriptional Regulation in Eukaryotes
    NIH R01GM041249Dec 1, 1988 - Dec 14, 2009
    Role: Principal Investigator
    Cell and Molecular Genetics Training Program
    NIH T32GM007240Jul 1, 1975 - Jun 30, 2021
    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. 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. 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:    Fields:    Translation:HumansCells
    2. Enhancement of homology-directed repair with chromatin donor templates in cells. Elife. 2020 Apr 28; 9. Cruz-Becerra G, Kadonaga JT. PMID: 32343230.
      View in: PubMed   Mentions:    Fields:    
    3. 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: 5     Fields:    Translation:AnimalsCells
    4. 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:    Fields:    Translation:Cells
    5. 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: 5     Fields:    Translation:AnimalsCells
    6. 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
    7. 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: 1     Fields:    Translation:AnimalsCells
    8. 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: 2     Fields:    Translation:HumansAnimalsCells
    9. 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: 4     Fields:    Translation:HumansAnimalsCells
    10. 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: 25     Fields:    Translation:AnimalsCells
    11. 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: 17     Fields:    Translation:HumansCells
    12. 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
    13. 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: 23     Fields:    Translation:HumansAnimalsCells
    14. 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
    15. 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: 22     Fields:    Translation:AnimalsCells
    16. 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: 52     Fields:    Translation:HumansCells
    17. 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: 9     Fields:    Translation:HumansAnimalsCells
    18. 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
    19. 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: 24     Fields:    Translation:AnimalsCells
    20. 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
    21. 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: 20     Fields:    Translation:HumansAnimalsCells
    22. 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
    23. 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: 60     Fields:    Translation:HumansCells
    24. 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: 68     Fields:    Translation:HumansAnimalsCells
    25. 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: 40     Fields:    Translation:Cells
    26. 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
    27. 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: 27     Fields:    Translation:HumansCells
    28. 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: 39     Fields:    Translation:Cells
    29. 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: 10     Fields:    Translation:HumansAnimalsCells
    30. 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: 23     Fields:    Translation:AnimalsCells
    31. 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: 77     Fields:    Translation:HumansAnimalsCells
    32. 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: 168     Fields:    Translation:HumansAnimalsCells
    33. 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: 197     Fields:    Translation:AnimalsCells
    34. 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: 31     Fields:    Translation:HumansCells
    35. 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: 92     Fields:    Translation:HumansCells
    36. 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
    37. 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
    38. 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: 372     Fields:    Translation:AnimalsCells
    39. 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: 157     Fields:    Translation:HumansAnimalsCells
    40. 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: 115     Fields:    Translation:AnimalsCells
    41. Perspectives on the RNA polymerase II core promoter. Biochem Soc Trans. 2006 Dec; 34(Pt 6):1047-50. Juven-Gershon T, Hsu JY, Kadonaga JT. PMID: 17073747.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    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: 73     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: 11     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: 33     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: 124     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: 33     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: 77     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: 144     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: 81     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: 98     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: 48     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: 371     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: 42     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: 60     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: 192     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: 37     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: 19     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: 39     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: 21     Fields:    Translation:AnimalsCells
    63. Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol Cell Biol. 2001 Oct; 21(19):6574-84. Tyler JK, Collins KA, Prasad-Sinha J, Amiott E, Bulger M, Harte PJ, Kobayashi R, Kadonaga JT. PMID: 11533245.
      View in: PubMed   Mentions: 102     Fields:    Translation:AnimalsCells
    64. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 2001 Oct 01; 15(19):2515-9. Butler JE, Kadonaga JT. PMID: 11581157.
      View in: PubMed   Mentions: 103     Fields:    Translation:AnimalsCells
    65. The many faces of chromatin remodeling: SWItching beyond transcription. Cell. 2001 Sep 07; 106(5):523-5. Fyodorov DV, Kadonaga JT. PMID: 11551498.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    66. p300 forms a stable, template-committed complex with chromatin: role for the bromodomain. Mol Cell Biol. 2001 Jun; 21(12):3876-87. Manning ET, Ikehara T, Ito T, Kadonaga JT, Kraus WL. PMID: 11359896.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    67. Purification of sequence-specific DNA-binding proteins by affinity chromatography. Curr Protoc Mol Biol. 2001 May; Chapter 12:Unit 12.10. Kerrigan LA, Kadonaga JT. PMID: 18265082.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    68. Purification of sequence-specific DNA-binding proteins by affinity chromatography. Curr Protoc Protein Sci. 2001 May; Chapter 9:Unit 9.6. Kerrigan LA, Kadonaga JT. PMID: 18429215.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    69. Biochemical analysis of transcriptional repression by Drosophila histone deacetylase 1. J Biol Chem. 2001 Apr 20; 276(16):12497-500. Huang X, Kadonaga JT. PMID: 11278256.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    70. Transcriptional analysis of chromatin assembled with purified ACF and dNAP1 reveals that acetyl-CoA is required for preinitiation complex assembly. J Biol Chem. 2000 Dec 22; 275(51):39819-22. Jiang W, Nordeen SK, Kadonaga JT. PMID: 11054407.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    71. A basal transcription factor that activates or represses transcription. Science. 2000 Nov 03; 290(5493):982-5. Willy PJ, Kobayashi R, Kadonaga JT. PMID: 11062130.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    72. Exploring the transcription-chromatin interface. Genes Dev. 2000 Aug 15; 14(16):1992-6. Jones KA, Kadonaga JT. PMID: 10950863.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    73. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol Cell Biol. 2000 Jul; 20(13):4754-64. Kutach AK, Kadonaga JT. PMID: 10848601.
      View in: PubMed   Mentions: 104     Fields:    Translation:AnimalsCells
    74. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 1999 Dec 02; 402(6761):555-60. Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT. PMID: 10591219.
      View in: PubMed   Mentions: 253     Fields:    Translation:HumansAnimalsCells
    75. Biochemical analysis of distinct activation functions in p300 that enhance transcription initiation with chromatin templates. Mol Cell Biol. 1999 Dec; 19(12):8123-35. Kraus WL, Manning ET, Kadonaga JT. PMID: 10567538.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansAnimalsCells
    76. The "dark side" of chromatin remodeling: repressive effects on transcription. Cell. 1999 Nov 24; 99(5):443-6. Tyler JK, Kadonaga JT. PMID: 10589670.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    77. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 1999 Jun 15; 13(12):1529-39. Ito T, Levenstein ME, Fyodorov DV, Kutach AK, Kobayashi R, Kadonaga JT. PMID: 10385622.
      View in: PubMed   Mentions: 131     Fields:    Translation:HumansAnimalsCells
    78. Promoter structure and transcriptional activation with chromatin templates assembled in vitro. A single Gal4-VP16 dimer binds to chromatin or to DNA with comparable affinity. J Biol Chem. 1998 Dec 18; 273(51):34653-60. Pazin MJ, Hermann JW, Kadonaga JT. PMID: 9852139.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    79. [Chromatin assembly and reconfiguration]. Tanpakushitsu Kakusan Koso. 1998 Nov; 43(14):2087-93. Ito T, Muramatsu M, Kadonaga JT. PMID: 9838850.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    80. Chromatin, TAFs, and a novel multiprotein coactivator are required for synergistic activation by Sp1 and SREBP-1a in vitro. Genes Dev. 1998 Oct 01; 12(19):3020-31. Näär AM, Beaurang PA, Robinson KM, Oliner JD, Avizonis D, Scheek S, Zwicker J, Kadonaga JT, Tjian R. PMID: 9765204.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansAnimalsCells
    81. The use of chromatin templates to recreate transcriptional regulatory phenomena in vitro. Biochim Biophys Acta. 1998 Aug 19; 1378(1):M1-6. Robinson KM, Kadonaga JT. PMID: 9739762.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    82. Going the distance: a current view of enhancer action. Science. 1998 Jul 03; 281(5373):60-3. Blackwood EM, Kadonaga JT. PMID: 9679020.
      View in: PubMed   Mentions: 257     Fields:    Translation:HumansAnimalsCells
    83. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell. 1998 Feb 06; 92(3):307-13. Kadonaga JT. PMID: 9476891.
      View in: PubMed   Mentions: 152     Fields:    Translation:AnimalsCells
    84. p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 1998 Feb 01; 12(3):331-42. Kraus WL, Kadonaga JT. PMID: 9450928.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansCells
    85. The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box. Cold Spring Harb Symp Quant Biol. 1998; 63:75-82. Burke TW, Willy PJ, Kutach AK, Butler JE, Kadonaga JT. PMID: 10384272.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    86. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 1997 Nov 15; 11(22):3020-31. Burke TW, Kadonaga JT. PMID: 9367984.
      View in: PubMed   Mentions: 181     Fields:    Translation:HumansAnimalsCells
    87. Chromatin assembly factors: a dual function in nucleosome formation and mobilization? Genes Cells. 1997 Oct; 2(10):593-600. Ito T, Tyler JK, Kadonaga JT. PMID: 9427281.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    88. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell. 1997 Jul 11; 90(1):145-55. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT. PMID: 9230310.
      View in: PubMed   Mentions: 217     Fields:    Translation:AnimalsCells
    89. Activation of RNA polymerase II by topologically linked DNA-tracking proteins. Proc Natl Acad Sci U S A. 1997 Jun 24; 94(13):6718-23. Ouhammouch M, Sayre MH, Kadonaga JT, Geiduschek EP. PMID: 9192631.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    90. Nucleosome mobility and the maintenance of nucleosome positioning. Science. 1997 May 02; 276(5313):809-12. Pazin MJ, Bhargava P, Geiduschek EP, Kadonaga JT. PMID: 9115208.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    91. What's up and down with histone deacetylation and transcription? Cell. 1997 May 02; 89(3):325-8. Pazin MJ, Kadonaga JT. PMID: 9150131.
      View in: PubMed   Mentions: 210     Fields:    Translation:AnimalsCells
    92. SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions? Cell. 1997 Mar 21; 88(6):737-40. Pazin MJ, Kadonaga JT. PMID: 9118215.
      View in: PubMed   Mentions: 93     Fields:    
    93. The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase-associated protein. Mol Cell Biol. 1996 Nov; 16(11):6149-59. Tyler JK, Bulger M, Kamakaka RT, Kobayashi R, Kadonaga JT. PMID: 8887645.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    94. ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. J Biol Chem. 1996 Oct 04; 271(40):25041-8. Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga JT. PMID: 8798787.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    95. Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays. Mol Cell Biol. 1996 Jun; 16(6):3112-24. Ito T, Bulger M, Kobayashi R, Kadonaga JT. PMID: 8649423.
      View in: PubMed   Mentions: 91     Fields:    Translation:AnimalsCells
    96. Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 1996 Mar 15; 10(6):711-24. Burke TW, Kadonaga JT. PMID: 8598298.
      View in: PubMed   Mentions: 137     Fields:    Translation:AnimalsCells
    97. Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol Cell Biol. 1996 Mar; 16(3):810-7. Kamakaka RT, Bulger M, Kaufman PD, Stillman B, Kadonaga JT. PMID: 8622682.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    98. NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro. Genes Dev. 1996 Jan 01; 10(1):37-49. Pazin MJ, Sheridan PL, Cannon K, Cao Z, Keck JG, Kadonaga JT, Jones KA. PMID: 8557193.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    99. Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein. Proc Natl Acad Sci U S A. 1995 Dec 05; 92(25):11726-30. Bulger M, Ito T, Kamakaka RT, Kadonaga JT. PMID: 8524837.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    100. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. Genes Dev. 1995 Sep 01; 9(17):2090-104. Sheridan PL, Sheline CT, Cannon K, Voz ML, Pazin MJ, Kadonaga JT, Jones KA. PMID: 7657162.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansAnimalsCells
    101. HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation. Genes Dev. 1995 Aug 15; 9(16):1978-91. Paranjape SM, Krumm A, Kadonaga JT. PMID: 7649479.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    102. Structure and function of the small subunit of TFIIF (RAP30) from Drosophila melanogaster. J Biol Chem. 1995 Mar 17; 270(11):6292-7. Frank DJ, Tyree CM, George CP, Kadonaga JT. PMID: 7890767.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    103. Structure of the genes encoding transcription factor IIB and TATA box-binding protein from Drosophila melanogaster. Gene. 1995 Feb 14; 153(2):203-7. Lira-DeVito LM, Burke TW, Kadonaga JT. PMID: 7875589.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    104. A spectrum of mechanisms for the assembly of the RNA polymerase II transcription preinitiation complex. Mol Cell Biol. 1995 Feb; 15(2):1049-59. George CP, Lira-DeVito LM, Wampler SL, Kadonaga JT. PMID: 7823920.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    105. ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. Science. 1994 Dec 23; 266(5193):2007-11. Pazin MJ, Kamakaka RT, Kadonaga JT. PMID: 7801129.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    106. Simian virus 40 origin- and T-antigen-dependent DNA replication with Drosophila factors in vitro. Mol Cell Biol. 1994 Aug; 14(8):5114-22. Kamakaka RT, Kaufman PD, Stillman B, Mitsis PG, Kadonaga JT. PMID: 8035793.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    107. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu Rev Biochem. 1994; 63:265-97. Paranjape SM, Kamakaka RT, Kadonaga JT. PMID: 7979240.
      View in: PubMed   Mentions: 109     Fields:    Translation:AnimalsCells
    108. The soluble nuclear fraction, a highly efficient transcription extract from Drosophila embryos. Methods Cell Biol. 1994; 44:225-35. Kamakaka RT, Kadonaga JT. PMID: 7707954.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    109. Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly. Genes Dev. 1993 Sep; 7(9):1779-95. Kamakaka RT, Bulger M, Kadonaga JT. PMID: 8370526.
      View in: PubMed   Mentions: 65     Fields:    Translation:AnimalsCells
    110. Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 1993 Jul; 7(7A):1254-65. Tyree CM, George CP, Lira-DeVito LM, Wampler SL, Dahmus ME, Zawel L, Kadonaga JT. PMID: 8319911.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    111. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Curr Opin Cell Biol. 1993 Jun; 5(3):417-23. Croston GE, Kadonaga JT. PMID: 8352958.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    112. In vivo and in vitro analysis of transcriptional activation mediated by the human cytomegalovirus major immediate-early proteins. Mol Cell Biol. 1993 Feb; 13(2):1238-50. Klucher KM, Sommer M, Kadonaga JT, Spector DH. PMID: 8423789.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    113. Biochemical analysis of the role of chromatin structure in the regulation of transcription by RNA polymerase II. Cold Spring Harb Symp Quant Biol. 1993; 58:205-12. Kamakaka RT, Kadonaga JT. PMID: 7956031.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    114. Periodic binding of individual core histones to DNA: inadvertent purification of the core histone H2B as a putative enhancer-binding factor. Nucleic Acids Res. 1992 Dec 25; 20(24):6673-80. Kerrigan LA, Kadonaga JT. PMID: 1480489.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    115. Mechanism of transcriptional antirepression by GAL4-VP16. Genes Dev. 1992 Dec; 6(12A):2270-81. Croston GE, Laybourn PJ, Paranjape SM, Kadonaga JT. PMID: 1459451.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    116. Threshold phenomena and long-distance activation of transcription by RNA polymerase II. Science. 1992 Sep 18; 257(5077):1682-5. Laybourn PJ, Kadonaga JT. PMID: 1388287.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    117. Functional analysis of Drosophila transcription factor IIB. Genes Dev. 1992 Aug; 6(8):1542-52. Wampler SL, Kadonaga JT. PMID: 1644295.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    118. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science. 1991 Oct 11; 254(5029):238-45. Laybourn PJ, Kadonaga JT. PMID: 1718039.
      View in: PubMed   Mentions: 149     Fields:    Translation:AnimalsCells
    119. A general method for purification of H1 histones that are active for repression of basal RNA polymerase II transcription. Protein Expr Purif. 1991 Apr-Jun; 2(2-3):162-9. Croston GE, Lira LM, Kadonaga JT. PMID: 1821786.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    120. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science. 1991 Feb 08; 251(4994):643-9. Croston GE, Kerrigan LA, Lira LM, Marshak DR, Kadonaga JT. PMID: 1899487.
      View in: PubMed   Mentions: 139     Fields:    Translation:HumansAnimalsCells
    121. Accurate and efficient RNA polymerase II transcription with a soluble nuclear fraction derived from Drosophila embryos. Proc Natl Acad Sci U S A. 1991 Feb 01; 88(3):1024-8. Kamakaka RT, Tyree CM, Kadonaga JT. PMID: 1992453.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    122. Sequence-specific transcriptional antirepression of the Drosophila Krüppel gene by the GAGA factor. J Biol Chem. 1991 Jan 05; 266(1):574-82. Kerrigan LA, Croston GE, Lira LM, Kadonaga JT. PMID: 1985916.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    123. Purification of sequence-specific binding proteins by DNA affinity chromatography. Methods Enzymol. 1991; 208:10-23. Kadonaga JT. PMID: 1779831.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    124. Fractionation of the general RNA polymerase II transcription factors from Drosophila embryos. J Biol Chem. 1990 Dec 05; 265(34):21223-31. Wampler SL, Tyree CM, Kadonaga JT. PMID: 2250021.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    125. Gene transcription: basal and regulated transcription by RNA polymerase II. Curr Opin Cell Biol. 1990 Jun; 2(3):496-501. Kadonaga JT. PMID: 2198898.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    126. Assembly and disassembly of the Drosophila RNA polymerase II complex during transcription. J Biol Chem. 1990 Feb 15; 265(5):2624-31. Kadonaga JT. PMID: 1689291.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    127. Distinct regions of Sp1 modulate DNA binding and transcriptional activation. Science. 1988 Dec 16; 242(4885):1566-70. Kadonaga JT, Courey AJ, Ladika J, Tjian R. PMID: 3059495.
      View in: PubMed   Mentions: 117     Fields:    Translation:HumansCells
    128. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell. 1987 Dec 24; 51(6):1079-90. Kadonaga JT, Carner KR, Masiarz FR, Tjian R. PMID: 3319186.
      View in: PubMed   Mentions: 469     Fields:    Translation:HumansCells
    129. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell. 1987 Jan 16; 48(1):79-89. Jones KA, Kadonaga JT, Rosenfeld PJ, Kelly TJ, Tjian R. PMID: 3024847.
      View in: PubMed   Mentions: 362     Fields:    Translation:HumansCells
    130. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 03; 234(4772):47-52. Briggs MR, Kadonaga JT, Bell SP, Tjian R. PMID: 3529394.
      View in: PubMed   Mentions: 415     Fields:    Translation:HumansAnimalsCells
    131. Affinity purification of sequence-specific DNA binding proteins. Proc Natl Acad Sci U S A. 1986 Aug; 83(16):5889-93. Kadonaga JT, Tjian R. PMID: 3461465.
      View in: PubMed   Mentions: 431     Fields:    Translation:HumansCells
    132. Binding of the Sp1 transcription factor by the human Harvey ras1 proto-oncogene promoter. Science. 1986 Jun 13; 232(4756):1410-3. Ishii S, Kadonaga JT, Tjian R, Brady JN, Merlino GT, Pastan I. PMID: 3012774.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    133. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 09; 232(4751):755-9. Jones KA, Kadonaga JT, Luciw PA, Tjian R. PMID: 3008338.
      View in: PubMed   Mentions: 278     Fields:    Translation:HumansCells
    134. Signal sequence mutants of beta-lactamase. J Biol Chem. 1985 Dec 25; 260(30):16192-9. Kadonaga JT, Plückthun A, Knowles JR. PMID: 3905810.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    135. Bidirectional SV40 transcription mediated by tandem Sp1 binding interactions. Science. 1985 Nov 01; 230(4725):511-7. Gidoni D, Kadonaga JT, Barrera-Saldaña H, Takahashi K, Chambon P, Tjian R. PMID: 2996137.
      View in: PubMed   Mentions: 128     Fields:    Translation:Cells
    136. A simple and efficient method for chemical mutagenesis of DNA. Nucleic Acids Res. 1985 Mar 11; 13(5):1733-45. Kadonaga JT, Knowles JR. PMID: 3889841.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    137. Dehydroquinate synthase from Escherichia coli: purification, cloning, and construction of overproducers of the enzyme. Biochemistry. 1984 Sep 11; 23(19):4470-5. Frost JW, Bender JL, Kadonaga JT, Knowles JR. PMID: 6386050.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    138. The role of the beta-lactamase signal sequence in the secretion of proteins by Escherichia coli. J Biol Chem. 1984 Feb 25; 259(4):2149-54. Kadonaga JT, Gautier AE, Straus DR, Charles AD, Edge MD, Knowles JR. PMID: 6365904.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    139. Role of mono- and divalent metal cations in the catalysis by yeast aldolase. Biochemistry. 1983 Jan 04; 22(1):130-6. Kadonaga JT, Knowles JR. PMID: 6338913.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
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