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James Kadonaga
Title
Researcher
School
University of California, San Diego
Department
Molecular Biology
Address
9500 Gilman Drive #0347
CA La Jolla 92093
Phone
858-534-4608
vCard
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Research
Research Activities and Funding
Mechanisms of Eukaryotic Gene Regulation
NIH/NIGMS
R35GM118060
May 1, 2016 - Apr 30, 2021
Role: Principal Investigator
Elucidation of Human TATA-less Transcription Networks
NIH/NHGRI
R21HG008781
Mar 22, 2016 - Dec 31, 2017
Role: Principal Investigator
Conference on Chromatin Structure and Activity
NIH/NCI
R13CA094873
Jan 10, 2002 - Dec 31, 2002
Role: Principal Investigator
Chromatin and DNA Dynamics
NIH/NIGMS
R01GM058272
Jan 1, 1999 - Jun 30, 2019
Role: Principal Investigator
Comprehensive Biology: Exploiting the Yeast Genome
NIH
P41RR011823
Sep 30, 1996 - Jun 30, 2016
Role: Co-Investigator
FASEB RESEARCH CONFERENCE--CHROMATIN AND TRANSCRIPTION
NIH/NIGMS
R13GM052603
Jun 1, 1995 - May 31, 1996
Role: Principal Investigator
CHROMATIN STRUCTURE AND GENE ACTIVITY
NIH/NIGMS
R01GM046995
Jul 1, 1992 - Nov 30, 2004
Role: Principal Investigator
Mechanisms of Transcriptional Regulation in Eukaryotes
NIH/NIGMS
R01GM041249
Dec 1, 1988 - Nov 30, 2017
Role: Principal Investigator
Cell and Molecular Genetics Training Program
NIH/NIGMS
T32GM007240
Jul 1, 1975 - Jun 30, 2020
Role: Principal Investigator
Bibliographic
Publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can
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Vo Ngoc L, Wang YL, Kassavetis GA,
Kadonaga J
. The punctilious RNA polymerase II core promoter. Genes Dev. 2017 Jul 01; 31(13):1289-1301. PMID: 28808065.
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PubMed
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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PubMed
Khuong MT, Fei J, Ishii H,
Kadonaga J
. Prenucleosomes and Active Chromatin. Cold Spring Harb Symp Quant Biol. 2015; 80:65-72. PMID: 26767995; PMCID: PMC4915978.
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PubMed
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PubMed Central
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; PMCID: PMC4699385.
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PubMed
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PubMed Central
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 05; 60(3):348-9. PMID: 26545075; PMCID: PMC4643650 [Available on 11/05/16].
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PubMed
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PubMed Central
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 07; 112(27):E3457-65. PMID: 26080409; PMCID: PMC4500276.
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PubMed
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PubMed Central
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; PMCID: PMC4336624.
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PubMed
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PubMed Central
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; PMCID: PMC4284531.
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PubMed
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PubMed Central
Duttke SH, Doolittle RF, Wang YL,
Kadonaga J
. TRF2 and the evolution of the bilateria. Genes Dev. 2014 Oct 01; 28(19):2071-6. PMID: 25274724; PMCID: PMC4180970.
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PubMed
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PubMed Central
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; PMCID: PMC4102762.
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PubMed
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PubMed Central
Kassavetis GA,
Kadonaga J
. The annealing helicase and branch migration activities of Drosophila HARP. PLoS One. 2014; 9(5):e98173. PMID: 24866343; PMCID: PMC4035279.
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PubMed
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PubMed Central
Torigoe SE, Patel A, Khuong MT, Bowman GD,
Kadonaga J
. ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. Elife. 2013 Aug 20; 2:e00863. PMID: 23986862; PMCID: PMC3748710.
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PubMed
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PubMed Central
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 08; 288(10):7096-104. PMID: 23349465; PMCID: PMC3591619.
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PubMed
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PubMed Central
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; PMCID: PMC3552382.
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PubMed
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PubMed Central
Kadonaga J
. Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb; 1(1):40-51. PMID: 23801666; PMCID: PMC3695423.
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PubMed
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PubMed Central
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; PMCID: PMC3160715.
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PubMed
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PubMed Central
Yusufzai T,
Kadonaga J
. Branching out with DNA helicases. Curr Opin Genet Dev. 2011 Apr; 21(2):214-8. PMID: 21324673; PMCID: PMC3079503.
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PubMed
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PubMed Central
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 07; 107(49):20970-3. PMID: 21078962; PMCID: PMC3000258.
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PubMed Central
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; PMCID: PMC2939363.
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PubMed
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PubMed Central
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; PMCID: PMC4742340.
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PubMed
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PubMed Central
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; PMCID: PMC2897566.
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PubMed
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PubMed Central
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; PMCID: PMC2764493.
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PubMed
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PubMed Central
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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PubMed
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; PMCID: PMC2823114.
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PubMed
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PubMed Central
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; PMCID: PMC2709789.
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PubMed
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PubMed Central
Yusufzai T,
Kadonaga J
. HARP is an ATP-driven annealing helicase. Science. 2008 Oct 31; 322(5902):748-50. PMID: 18974355; PMCID: PMC2587503.
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PubMed
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PubMed Central
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; PMCID: PMC2569877.
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PubMed
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PubMed Central
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 01; 22(17):2353-8. PMID: 18703680; PMCID: PMC2532932.
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PubMed
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PubMed Central
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; PMCID: PMC2447866.
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PubMed
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PubMed Central
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; PMCID: PMC2586601.
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PubMed
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PubMed Central
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; PMCID: PMC3014568.
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PubMed
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PubMed Central
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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PubMed
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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PubMed
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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PubMed
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; PMCID: PMC1306797.
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PubMed
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PubMed Central
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 05; 351(1):89-99. PMID: 16002089.
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PubMed
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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PubMed
Lusser A,
Kadonaga J
. Strategies for the reconstitution of chromatin. Nat Methods. 2004 Oct; 1(1):19-26. PMID: 15789029.
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PubMed
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 01; 18(13):1606-17. PMID: 15231738; PMCID: PMC443522.
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PubMed
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PubMed Central
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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PubMed
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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PubMed
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; PMCID: PMC324423.
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PubMed
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PubMed Central
Lusser A,
Kadonaga J
. Chromatin remodeling by ATP-dependent molecular machines. Bioessays. 2003 Dec; 25(12):1192-200. PMID: 14635254.
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PubMed
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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PubMed
Smale ST,
Kadonaga J
. The RNA polymerase II core promoter. Annu Rev Biochem. 2003; 72:449-79. PMID: 12651739.
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PubMed
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; PMCID: PMC149880.
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PubMed
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PubMed Central
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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PubMed
Alexiadis V,
Kadonaga J
. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 2002 Nov 01; 16(21):2767-71. PMID: 12414729; PMCID: PMC187467.
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PubMed
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PubMed Central
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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PubMed
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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PubMed
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; PMCID: PMC135643.
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PubMed
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PubMed Central
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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PubMed
Levenstein ME,
Kadonaga J
. Biochemical analysis of chromatin containing recombinant Drosophila core histones. J Biol Chem. 2002 Mar 08; 277(10):8749-54. PMID: 11773058.
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PubMed
Butler JE,
Kadonaga J
. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 2001 Oct 01; 15(19):2515-9. PMID: 11581157; PMCID: PMC312797.
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PubMed
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PubMed Central
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; PMCID: PMC99803.
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PubMed
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PubMed Central
Fyodorov DV,
Kadonaga J
. The many faces of chromatin remodeling: SWItching beyond transcription. Cell. 2001 Sep 07; 106(5):523-5. PMID: 11551498.
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PubMed
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; PMCID: PMC87051.
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PubMed
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PubMed Central
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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PubMed
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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PubMed
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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PubMed
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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PubMed
Willy PJ, Kobayashi R,
Kadonaga J
. A basal transcription factor that activates or represses transcription. Science. 2000 Nov 03; 290(5493):982-5. PMID: 11062130.
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PubMed
Jones KA,
Kadonaga J
. Exploring the transcription-chromatin interface. Genes Dev. 2000 Aug 15; 14(16):1992-6. PMID: 10950863.
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PubMed
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; PMCID: PMC85905.
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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 02; 402(6761):555-60. PMID: 10591219.
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PubMed
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; PMCID: PMC84897.
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PubMed Central
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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PubMed
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; PMCID: PMC316812.
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PubMed Central
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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PubMed
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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PubMed
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 01; 12(19):3020-31. PMID: 9765204; PMCID: PMC317191.
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PubMed Central
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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PubMed
Blackwood EM,
Kadonaga J
. Going the distance: a current view of enhancer action. Science. 1998 Jul 03; 281(5373):60-3. PMID: 9679020.
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PubMed
Kadonaga J
. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell. 1998 Feb 06; 92(3):307-13. PMID: 9476891.
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PubMed
Kraus WL,
Kadonaga J
. p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 1998 Feb 01; 12(3):331-42. PMID: 9450928; PMCID: PMC316488.
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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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PubMed
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; PMCID: PMC316699.
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PubMed Central
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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PubMed
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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PubMed
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; PMCID: PMC21224.
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PubMed
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PubMed Central
Pazin MJ,
Kadonaga J
. What's up and down with histone deacetylation and transcription? Cell. 1997 May 02; 89(3):325-8. PMID: 9150131.
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PubMed
Pazin MJ, Bhargava P, Geiduschek EP,
Kadonaga J
. Nucleosome mobility and the maintenance of nucleosome positioning. Science. 1997 May 02; 276(5313):809-12. PMID: 9115208.
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PubMed
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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PubMed
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; PMCID: PMC231618.
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PubMed Central
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 04; 271(40):25041-8. PMID: 8798787.
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PubMed
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; PMCID: PMC231306.
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PubMed Central
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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PubMed
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; PMCID: PMC231061.
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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 01; 10(1):37-49. PMID: 8557193.
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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 05; 92(25):11726-30. PMID: 8524837; PMCID: PMC40475.
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PubMed Central
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 01; 9(17):2090-104. PMID: 7657162.
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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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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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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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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; PMCID: PMC232004.
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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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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; PMCID: PMC359030.
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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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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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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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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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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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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; PMCID: PMC359009.
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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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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; PMCID: PMC334585.
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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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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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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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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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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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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 08; 251(4994):643-9. PMID: 1899487.
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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 01; 88(3):1024-8. PMID: 1992453; PMCID: PMC50947.
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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 05; 266(1):574-82. PMID: 1985916.
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Kadonaga J
. Purification of sequence-specific binding proteins by DNA affinity chromatography. Methods Enzymol. 1991; 208:10-23. PMID: 1779831.
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Wampler SL, Tyree CM,
Kadonaga J
. Fractionation of the general RNA polymerase II transcription factors from Drosophila embryos. J Biol Chem. 1990 Dec 05; 265(34):21223-31. PMID: 2250021.
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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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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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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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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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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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Briggs MR,
Kadonaga J
, Bell SP, Tjian R. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 03; 234(4772):47-52. PMID: 3529394.
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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; PMCID: PMC386402.
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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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Jones KA,
Kadonaga J
, Luciw PA, Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 09; 232(4751):755-9. PMID: 3008338.
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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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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 01; 230(4725):511-7. PMID: 2996137.
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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; PMCID: PMC341108.
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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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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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Kadonaga J
, Knowles JR. Role of mono- and divalent metal cations in the catalysis by yeast aldolase. Biochemistry. 1983 Jan 04; 22(1):130-6. PMID: 6338913.
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James's Networks
Concepts
Derived automatically from this person's publications.
RNA Polymerase II
Chromatin
Nucleosomes
Promoter Regions, Genetic
Transcription, Genetic
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Duttke, Sascha
Fei, Jia
Wang, Dong
Vo Ngoc, Long
Doolittle, Russell
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