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    James Kadonaga

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentMolecular Biology
    Address9500 Gilman Drive #0347
    CA La Jolla 92093
    Phone858-534-4608
    vCardDownload vCard

      Collapse Research 
      Collapse Research Activities and Funding
      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 - 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 R13GM052603Jun 1, 1995 - May 31, 1996
      Role: Principal Investigator
      CHROMATIN STRUCTURE AND GENE ACTIVITY
      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, 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.
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      1. Vo Ngoc L, Cassidy CJ, Huang CY, Duttke SH, Kadonaga J. The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. Genes Dev. 2017 Jan 01; 31(1):6-11. PMID: 28108474.
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      2. Khuong MT, Fei J, Ishii H, Kadonaga J. Prenucleosomes and Active Chromatin. Cold Spring Harb Symp Quant Biol. 2015; 80:65-72. PMID: 26767995.
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      3. Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga J. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev. 2015 Dec 15; 29(24):2563-75. PMID: 26680301.
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      4. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga J, Ohler U. Perspectives on Unidirectional versus Divergent Transcription. Mol Cell. 2015 Nov 5; 60(3):348-9. PMID: 26545075.
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      5. Ishii H, Kadonaga J, Ren B. MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A. 2015 Jul 7; 112(27):E3457-65. PMID: 26080409.
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      6. Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga J, Ohler U. Human promoters are intrinsically directional. Mol Cell. 2015 Feb 19; 57(4):674-84. PMID: 25639469.
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      7. Wang L, Limbo O, Fei J, Chen L, Kim B, Luo J, Chong J, Conaway RC, Conaway JW, Ranish JA, Kadonaga J, 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.
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      8. Duttke SH, Doolittle RF, Wang YL, Kadonaga J. TRF2 and the evolution of the bilateria. Genes Dev. 2014 Oct 1; 28(19):2071-6. PMID: 25274724.
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      9. Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga J. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 2014 Jul 15; 28(14):1550-5. PMID: 24958592.
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      10. Kassavetis GA, Kadonaga J. The Annealing Helicase and Branch Migration Activities of Drosophila HARP. PLoS One. 2014; 9(5):e98173. PMID: 24866343.
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      11. Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga J. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. Elife. 2013; 2:e00863. PMID: 23986862.
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      12. Theisen JW, Gucwa JS, Yusufzai T, Khuong MT, Kadonaga J. Biochemical analysis of histone deacetylase-independent transcriptional repression by MeCP2. J Biol Chem. 2013 Mar 8; 288(10):7096-104. PMID: 23349465.
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      13. Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga J, 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.
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      14. Kadonaga J. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb; 1(1):40-51. PMID: 23801666.
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      15. Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga J. 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.
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      16. Yusufzai T, Kadonaga J. Branching out with DNA helicases. Curr Opin Genet Dev. 2011 Apr; 21(2):214-8. PMID: 21324673.
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      17. Yusufzai T, Kadonaga J. Annealing helicase 2 (AH2), a DNA-rewinding motor with an HNH motif. Proc Natl Acad Sci U S A. 2010 Dec 7; 107(49):20970-3. PMID: 21078962.
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      18. Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga J. 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.
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      19. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga J, 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.
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      20. Theisen JW, Lim CY, Kadonaga J. 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.
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      21. Yusufzai T, Kong X, Yokomori K, Kadonaga J. 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.
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      22. Juven-Gershon T, Kadonaga J. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol. 2010 Mar 15; 339(2):225-9. PMID: 19682982.
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      23. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga J, 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.
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      24. Rattner BP, Yusufzai T, Kadonaga J. 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.
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      25. Yusufzai T, Kadonaga J. HARP is an ATP-driven annealing helicase. Science. 2008 Oct 31; 322(5902):748-50. PMID: 18974355.
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      26. Juven-Gershon T, Hsu JY, Kadonaga J. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev. 2008 Oct 15; 22(20):2823-30. PMID: 18923080.
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      27. Hsu JY, Juven-Gershon T, Marr MT, Wright KJ, Tjian R, Kadonaga J. TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes Dev. 2008 Sep 1; 22(17):2353-8. PMID: 18703680.
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      28. 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 J, 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.
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      29. Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga J. The RNA polymerase II core promoter - the gateway to transcription. Curr Opin Cell Biol. 2008 Jun; 20(3):253-9. PMID: 18436437.
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      30. Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga J, 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.
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      31. Juven-Gershon T, Hsu JY, Kadonaga J. Perspectives on the RNA polymerase II core promoter. Biochem Soc Trans. 2006 Dec; 34(Pt 6):1047-50. PMID: 17073747.
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      32. Juven-Gershon T, Cheng S, Kadonaga J. 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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      33. Santoso B, Kadonaga J. 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.
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      34. Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen'ev MB, Kadonaga J, 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.
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      35. Gemmen GJ, Sim R, Haushalter KA, Ke PC, Kadonaga J, Smith DE. Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF. J Mol Biol. 2005 Aug 5; 351(1):89-99. PMID: 16002089.
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      36. Lusser A, Urwin DL, Kadonaga J. 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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      37. Lusser A, Kadonaga J. Strategies for the reconstitution of chromatin. Nat Methods. 2004 Oct; 1(1):19-26. PMID: 15789029.
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      38. Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga J. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 2004 Jul 1; 18(13):1606-17. PMID: 15231738.
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      39. Alexiadis V, Lusser A, Kadonaga J. 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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      40. Kadonaga J. 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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      41. Fyodorov DV, Blower MD, Karpen GH, Kadonaga J. 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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      42. Lusser A, Kadonaga J. Chromatin remodeling by ATP-dependent molecular machines. Bioessays. 2003 Dec; 25(12):1192-200. PMID: 14635254.
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      43. Haushalter KA, Kadonaga J. Chromatin assembly by DNA-translocating motors. Nat Rev Mol Cell Biol. 2003 Aug; 4(8):613-20. PMID: 12923523.
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      44. Smale ST, Kadonaga J. The RNA polymerase II core promoter. Annu Rev Biochem. 2003; 72:449-79. PMID: 12651739.
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      45. Parsons XH, Garcia SN, Pillus L, Kadonaga J. 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.
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      46. Fyodorov DV, Kadonaga J. Chromatin assembly in vitro with purified recombinant ACF and NAP-1. Methods Enzymol. 2003; 371:499-515. PMID: 14712724.
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      47. Alexiadis V, Kadonaga J. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 2002 Nov 1; 16(21):2767-71. PMID: 12414729.
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      48. Butler JE, Kadonaga J. 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.
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      49. Kadonaga J. The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med. 2002 Sep 30; 34(4):259-64. PMID: 12515390.
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      50. Fyodorov DV, Kadonaga J. 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.
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      51. Fyodorov DV, Kadonaga J. Dynamics of ATP-dependent chromatin assembly by ACF. Nature. 2002 Aug 22; 418(6900):897-900. PMID: 12192415.
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      52. Levenstein ME, Kadonaga J. Biochemical analysis of chromatin containing recombinant Drosophila core histones. J Biol Chem. 2002 Mar 8; 277(10):8749-54. PMID: 11773058.
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      53. Butler JE, Kadonaga J. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 2001 Oct 1; 15(19):2515-9. PMID: 11581157.
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      54. Tyler JK, Collins KA, Prasad-Sinha J, Amiott E, Bulger M, Harte PJ, Kobayashi R, Kadonaga J. Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol Cell Biol. 2001 Oct; 21(19):6574-84. PMID: 11533245.
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      55. Fyodorov DV, Kadonaga J. The many faces of chromatin remodeling: SWItching beyond transcription. Cell. 2001 Sep 7; 106(5):523-5. PMID: 11551498.
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      56. Manning ET, Ikehara T, Ito T, Kadonaga J, Kraus WL. p300 forms a stable, template-committed complex with chromatin: role for the bromodomain. Mol Cell Biol. 2001 Jun; 21(12):3876-87. PMID: 11359896.
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      57. Kerrigan LA, Kadonaga J. Purification of sequence-specific DNA-binding proteins by affinity chromatography. Curr Protoc Protein Sci. 2001 May; Chapter 9:Unit 9.6. PMID: 18429215.
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      58. Kerrigan LA, Kadonaga J. Purification of sequence-specific DNA-binding proteins by affinity chromatography. Curr Protoc Mol Biol. 2001 May; Chapter 12:Unit 12.10. PMID: 18265082.
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      59. Huang X, Kadonaga J. Biochemical analysis of transcriptional repression by Drosophila histone deacetylase 1. J Biol Chem. 2001 Apr 20; 276(16):12497-500. PMID: 11278256.
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      60. Jiang W, Nordeen SK, Kadonaga J. 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. PMID: 11054407.
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      61. Willy PJ, Kobayashi R, Kadonaga J. A basal transcription factor that activates or represses transcription. Science. 2000 Nov 3; 290(5493):982-5. PMID: 11062130.
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      62. Jones KA, Kadonaga J. Exploring the transcription-chromatin interface. Genes Dev. 2000 Aug 15; 14(16):1992-6. PMID: 10950863.
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      63. Kutach AK, Kadonaga J. 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. PMID: 10848601.
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      64. Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga J. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 1999 Dec 2; 402(6761):555-60. PMID: 10591219.
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      65. Kraus WL, Manning ET, Kadonaga J. Biochemical analysis of distinct activation functions in p300 that enhance transcription initiation with chromatin templates. Mol Cell Biol. 1999 Dec; 19(12):8123-35. PMID: 10567538.
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      66. Tyler JK, Kadonaga J. The "dark side" of chromatin remodeling: repressive effects on transcription. Cell. 1999 Nov 24; 99(5):443-6. PMID: 10589670.
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      67. Ito T, Levenstein ME, Fyodorov DV, Kutach AK, Kobayashi R, Kadonaga J. 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. PMID: 10385622.
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      68. Pazin MJ, Hermann JW, Kadonaga J. 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. PMID: 9852139.
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      69. Ito T, Muramatsu M, Kadonaga J. [Chromatin assembly and reconfiguration]. Tanpakushitsu Kakusan Koso. 1998 Nov; 43(14):2087-93. PMID: 9838850.
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      70. Näär AM, Beaurang PA, Robinson KM, Oliner JD, Avizonis D, Scheek S, Zwicker J, Kadonaga J, Tjian R. Chromatin, TAFs, and a novel multiprotein coactivator are required for synergistic activation by Sp1 and SREBP-1a in vitro. Genes Dev. 1998 Oct 1; 12(19):3020-31. PMID: 9765204.
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      71. Robinson KM, Kadonaga J. The use of chromatin templates to recreate transcriptional regulatory phenomena in vitro. Biochim Biophys Acta. 1998 Aug 19; 1378(1):M1-6. PMID: 9739762.
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      72. Blackwood EM, Kadonaga J. Going the distance: a current view of enhancer action. Science. 1998 Jul 3; 281(5373):60-3. PMID: 9679020.
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      73. Kadonaga J. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell. 1998 Feb 6; 92(3):307-13. PMID: 9476891.
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      74. Kraus WL, Kadonaga J. p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 1998 Feb 1; 12(3):331-42. PMID: 9450928.
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      75. Burke TW, Willy PJ, Kutach AK, Butler JE, Kadonaga J. 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. PMID: 10384272.
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      76. Burke TW, Kadonaga J. 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. PMID: 9367984.
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      77. Ito T, Tyler JK, Kadonaga J. Chromatin assembly factors: a dual function in nucleosome formation and mobilization? Genes Cells. 1997 Oct; 2(10):593-600. PMID: 9427281.
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      78. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga J. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell. 1997 Jul 11; 90(1):145-55. PMID: 9230310.
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      79. Ouhammouch M, Sayre MH, Kadonaga J, Geiduschek EP. 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. PMID: 9192631.
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      80. Pazin MJ, Kadonaga J. What's up and down with histone deacetylation and transcription? Cell. 1997 May 2; 89(3):325-8. PMID: 9150131.
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      81. Pazin MJ, Bhargava P, Geiduschek EP, Kadonaga J. Nucleosome mobility and the maintenance of nucleosome positioning. Science. 1997 May 2; 276(5313):809-12. PMID: 9115208.
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      82. Pazin MJ, Kadonaga J. SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions? Cell. 1997 Mar 21; 88(6):737-40. PMID: 9118215.
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      83. Tyler JK, Bulger M, Kamakaka RT, Kobayashi R, Kadonaga J. 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. PMID: 8887645.
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      84. Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga J. ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. J Biol Chem. 1996 Oct 4; 271(40):25041-8. PMID: 8798787.
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      85. Ito T, Bulger M, Kobayashi R, Kadonaga J. 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. PMID: 8649423.
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      86. Burke TW, Kadonaga J. 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. PMID: 8598298.
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      87. Kamakaka RT, Bulger M, Kaufman PD, Stillman B, Kadonaga J. Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol Cell Biol. 1996 Mar; 16(3):810-7. PMID: 8622682.
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      88. Pazin MJ, Sheridan PL, Cannon K, Cao Z, Keck JG, Kadonaga J, Jones KA. NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro. Genes Dev. 1996 Jan 1; 10(1):37-49. PMID: 8557193.
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      89. Bulger M, Ito T, Kamakaka RT, Kadonaga J. 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 5; 92(25):11726-30. PMID: 8524837.
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      90. Sheridan PL, Sheline CT, Cannon K, Voz ML, Pazin MJ, Kadonaga J, Jones KA. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. Genes Dev. 1995 Sep 1; 9(17):2090-104. PMID: 7657162.
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      91. Paranjape SM, Krumm A, Kadonaga J. HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation. Genes Dev. 1995 Aug 15; 9(16):1978-91. PMID: 7649479.
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      92. Frank DJ, Tyree CM, George CP, Kadonaga J. Structure and function of the small subunit of TFIIF (RAP30) from Drosophila melanogaster. J Biol Chem. 1995 Mar 17; 270(11):6292-7. PMID: 7890767.
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      93. Lira-DeVito LM, Burke TW, Kadonaga J. Structure of the genes encoding transcription factor IIB and TATA box-binding protein from Drosophila melanogaster. Gene. 1995 Feb 14; 153(2):203-7. PMID: 7875589.
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      94. George CP, Lira-DeVito LM, Wampler SL, Kadonaga J. A spectrum of mechanisms for the assembly of the RNA polymerase II transcription preinitiation complex. Mol Cell Biol. 1995 Feb; 15(2):1049-59. PMID: 7823920.
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      95. Pazin MJ, Kamakaka RT, Kadonaga J. ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. Science. 1994 Dec 23; 266(5193):2007-11. PMID: 7801129.
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      96. Kamakaka RT, Kaufman PD, Stillman B, Mitsis PG, Kadonaga J. Simian virus 40 origin- and T-antigen-dependent DNA replication with Drosophila factors in vitro. Mol Cell Biol. 1994 Aug; 14(8):5114-22. PMID: 8035793.
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      97. Kamakaka RT, Kadonaga J. The soluble nuclear fraction, a highly efficient transcription extract from Drosophila embryos. Methods Cell Biol. 1994; 44:225-35. PMID: 7707954.
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      98. Paranjape SM, Kamakaka RT, Kadonaga J. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu Rev Biochem. 1994; 63:265-97. PMID: 7979240.
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      99. Kamakaka RT, Bulger M, Kadonaga J. 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. PMID: 8370526.
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      100. Tyree CM, George CP, Lira-DeVito LM, Wampler SL, Dahmus ME, Zawel L, Kadonaga J. 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. PMID: 8319911.
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      101. Croston GE, Kadonaga J. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Curr Opin Cell Biol. 1993 Jun; 5(3):417-23. PMID: 8352958.
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      102. Klucher KM, Sommer M, Kadonaga J, Spector DH. 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. PMID: 8423789.
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      103. Kamakaka RT, Kadonaga J. 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. PMID: 7956031.
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      104. Kerrigan LA, Kadonaga J. 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. PMID: 1480489.
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      105. Croston GE, Laybourn PJ, Paranjape SM, Kadonaga J. Mechanism of transcriptional antirepression by GAL4-VP16. Genes Dev. 1992 Dec; 6(12A):2270-81. PMID: 1459451.
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      106. Laybourn PJ, Kadonaga J. Threshold phenomena and long-distance activation of transcription by RNA polymerase II. Science. 1992 Sep 18; 257(5077):1682-5. PMID: 1388287.
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      107. Wampler SL, Kadonaga J. Functional analysis of Drosophila transcription factor IIB. Genes Dev. 1992 Aug; 6(8):1542-52. PMID: 1644295.
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      108. Laybourn PJ, Kadonaga J. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science. 1991 Oct 11; 254(5029):238-45. PMID: 1718039.
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      109. Croston GE, Lira LM, Kadonaga J. 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. PMID: 1821786.
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      110. Croston GE, Kerrigan LA, Lira LM, Marshak DR, Kadonaga J. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science. 1991 Feb 8; 251(4994):643-9. PMID: 1899487.
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      111. Kamakaka RT, Tyree CM, Kadonaga J. 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 1; 88(3):1024-8. PMID: 1992453.
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      112. Kerrigan LA, Croston GE, Lira LM, Kadonaga J. Sequence-specific transcriptional antirepression of the Drosophila Krüppel gene by the GAGA factor. J Biol Chem. 1991 Jan 5; 266(1):574-82. PMID: 1985916.
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      113. Kadonaga J. Purification of sequence-specific binding proteins by DNA affinity chromatography. Methods Enzymol. 1991; 208:10-23. PMID: 1779831.
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      114. Wampler SL, Tyree CM, Kadonaga J. Fractionation of the general RNA polymerase II transcription factors from Drosophila embryos. J Biol Chem. 1990 Dec 5; 265(34):21223-31. PMID: 2250021.
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      115. Kadonaga J. Gene transcription: basal and regulated transcription by RNA polymerase II. Curr Opin Cell Biol. 1990 Jun; 2(3):496-501. PMID: 2198898.
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      116. Kadonaga J. Assembly and disassembly of the Drosophila RNA polymerase II complex during transcription. J Biol Chem. 1990 Feb 15; 265(5):2624-31. PMID: 1689291.
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      117. Kadonaga J, Courey AJ, Ladika J, Tjian R. Distinct regions of Sp1 modulate DNA binding and transcriptional activation. Science. 1988 Dec 16; 242(4885):1566-70. PMID: 3059495.
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      118. Kadonaga J, Carner KR, Masiarz FR, Tjian R. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell. 1987 Dec 24; 51(6):1079-90. PMID: 3319186.
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      119. Jones KA, Kadonaga J, Rosenfeld PJ, Kelly TJ, Tjian R. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell. 1987 Jan 16; 48(1):79-89. PMID: 3024847.
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      120. Briggs MR, Kadonaga J, Bell SP, Tjian R. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 3; 234(4772):47-52. PMID: 3529394.
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      121. Kadonaga J, Tjian R. Affinity purification of sequence-specific DNA binding proteins. Proc Natl Acad Sci U S A. 1986 Aug; 83(16):5889-93. PMID: 3461465.
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      122. Ishii S, Kadonaga J, Tjian R, Brady JN, Merlino GT, Pastan I. Binding of the Sp1 transcription factor by the human Harvey ras1 proto-oncogene promoter. Science. 1986 Jun 13; 232(4756):1410-3. PMID: 3012774.
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      123. Jones KA, Kadonaga J, Luciw PA, Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 9; 232(4751):755-9. PMID: 3008338.
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      124. Kadonaga J, Plückthun A, Knowles JR. Signal sequence mutants of beta-lactamase. J Biol Chem. 1985 Dec 25; 260(30):16192-9. PMID: 3905810.
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      125. Gidoni D, Kadonaga J, Barrera-Saldaña H, Takahashi K, Chambon P, Tjian R. Bidirectional SV40 transcription mediated by tandem Sp1 binding interactions. Science. 1985 Nov 1; 230(4725):511-7. PMID: 2996137.
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      126. Kadonaga J, Knowles JR. A simple and efficient method for chemical mutagenesis of DNA. Nucleic Acids Res. 1985 Mar 11; 13(5):1733-45. PMID: 3889841.
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      127. Frost JW, Bender JL, Kadonaga J, Knowles JR. Dehydroquinate synthase from Escherichia coli: purification, cloning, and construction of overproducers of the enzyme. Biochemistry. 1984 Sep 11; 23(19):4470-5. PMID: 6386050.
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      128. Kadonaga J, Gautier AE, Straus DR, Charles AD, Edge MD, Knowles JR. 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. PMID: 6365904.
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      129. Kadonaga J, Knowles JR. Role of mono- and divalent metal cations in the catalysis by yeast aldolase. Biochemistry. 1983 Jan 4; 22(1):130-6. PMID: 6338913.
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