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James Kadonaga

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Co-Publications
Name
11
Kamakaka, Rohinton
8
Pazin, MJ
7
Fyodorov, Dmitry
6
Tyler, JK
5
Lusser, Alexandra
4
Tyree, Curtis
3
Kutach, Alan K.
3
Ito, T
3
Kraus, Lee
2
Jones, Katherine
2
Hsu, Jer-Yuan
2
Geiduschek, Peter
2
Tjian, Robert
1
Tora, Làszlò
1
Karpen, Gary

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Publications

TOP 3
Yusufzai Timur; Kong Xiangduo; Yokomori Kyoko; Kadonaga James T
The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA.
Zhang Yong; Moqtaderi Zarmik; Rattner Barbara P; Euskirchen Ghia; Snyder Michael; Kadonaga James T; Liu X Shirley; Struhl Kevin
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
Rattner Barbara P; Yusufzai Timur; Kadonaga James T
HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility.

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All Publications

2009: Yusufzai Timur; Kong Xiangduo; Yokomori Kyoko; Kadonaga James T
The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA.
Genes & development 2009;23(20):2400-4.
2009: Zhang Yong; Moqtaderi Zarmik; Rattner Barbara P; Euskirchen Ghia; Snyder Michael; Kadonaga James T; Liu X Shirley; Struhl Kevin
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
Nature structural & molecular biology 2009;16(8):847-52.
2009: Rattner Barbara P; Yusufzai Timur; Kadonaga James T
HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility.
Molecular cell 2009;34(5):620-6.
2008: Yusufzai Timur; Kadonaga James T
HARP is an ATP-driven annealing helicase.
Science (New York, N.Y.) 2008;322(5902):748-50.
2008: Juven-Gershon Tamar; Hsu Jer-Yuan; Kadonaga James T
Caudal, a key developmental regulator, is a DPE-specific transcriptional factor.
Genes & development 2008;22(20):2823-30.
2008: Hsu Jer-Yuan; Juven-Gershon Tamar; Marr Michael T; Wright Kevin J; Tjian Robert; Kadonaga James T
TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.
Genes & development 2008;22(17):2353-8.
2008: Pfeiffer Barret D; Jenett Arnim; Hammonds Ann S; Ngo Teri-T B; Misra Sima; Murphy Christine; Scully Audra; Carlson Joseph W; Wan Kenneth H; Laverty Todd R; Mungall Chris; Svirskas Rob; Kadonaga James T; Doe Chris Q; Eisen Michael B; Celniker Susan E; Rubin Gerald M
Tools for neuroanatomy and neurogenetics in Drosophila.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(28):9715-20.
2008: Juven-Gershon Tamar; Hsu Jer-Yuan; Theisen Joshua Wm; Kadonaga James T
The RNA polymerase II core promoter - the gateway to transcription.
Current opinion in cell biology 2008;20(3):253-9.
2007: Konev Alexander Y; Tribus Martin; Park Sung Yeon; Podhraski Valerie; Lim Chin Yan; Emelyanov Alexander V; Vershilova Elena; Pirrotta Vincenzo; Kadonaga James T; Lusser Alexandra; Fyodorov Dmitry V
CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo.
Science (New York, N.Y.) 2007;317(5841):1087-90.
2006: Juven-Gershon T; Hsu J-Y; Kadonaga J T
Perspectives on the RNA polymerase II core promoter.
Biochemical Society transactions 2006;34(Pt 6):1047-50.
2006: Juven-Gershon Tamar; Cheng Susan; Kadonaga James T
Rational design of a super core promoter that enhances gene expression.
Nature methods 2006;3(11):917-22.
2006: Santoso Buyung; Kadonaga James T
Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300.
Nature structural & molecular biology 2006;13(2):131-9.
2005: Lebedeva Lyubov A; Nabirochkina Elena N; Kurshakova Mariya M; Robert Flavie; Krasnov Aleksey N; Evgen'ev Mihail B; Kadonaga James T; Georgieva Sofia G; Tora Làszlò
Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(50):18087-92.
2005: Gemmen Gregory J; Sim Ronald; Haushalter Karl A; Ke Pu Chun; Kadonaga James T; Smith Douglas E
Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF.
Journal of molecular biology 2005;351(1):89-99.
2005: Lusser Alexandra; Urwin Debra L; Kadonaga James T
Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly.
Nature structural & molecular biology 2005;12(2):160-6.
2004: Lusser Alexandra; Kadonaga James T
Strategies for the reconstitution of chromatin.
Nature methods 2004;1(1):19-26.
2004: Lim Chin Yan; Santoso Buyung; Boulay Thomas; Dong Emily; Ohler Uwe; Kadonaga James T
The MTE, a new core promoter element for transcription by RNA polymerase II.
Genes & development 2004;18(13):1606-17.
2004: Alexiadis Vassilios; Lusser Alexandra; Kadonaga James T
A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing.
The Journal of biological chemistry 2004;279(26):27824-9.
2004: Fyodorov Dmitry V; Blower Michael D; Karpen Gary H; Kadonaga James T
Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo.
Genes & development 2004;18(2):170-83.
2004: Kadonaga James T
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.
Cell 2004;116(2):247-57.
2003: Lusser Alexandra; Kadonaga James T
Chromatin remodeling by ATP-dependent molecular machines.
BioEssays : news and reviews in molecular, cellular and developmental biology 2003;25(12):1192-200.
2003: Haushalter Karl A; Kadonaga James T
Chromatin assembly by DNA-translocating motors.
Nature reviews. Molecular cell biology 2003;4(8):613-20.
2003: Parsons Xuejun Huang; Garcia Sandra N; Pillus Lorraine; Kadonaga James T
Histone deacetylation by Sir2 generates a transcriptionally repressed nucleoprotein complex.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(4):1609-14.
2003: Fyodorov Dmitry V; Kadonaga James T
Chromatin assembly in vitro with purified recombinant ACF and NAP-1.
Methods in enzymology 2003;371():499-515.
2003: Smale Stephen T; Kadonaga James T
The RNA polymerase II core promoter.
Annual review of biochemistry 2003;72():449-79.
2002: Alexiadis Vassilios; Kadonaga James T
Strand pairing by Rad54 and Rad51 is enhanced by chromatin.
Genes & development 2002;16(21):2767-71.
2002: Butler Jennifer E F; Kadonaga James T
The RNA polymerase II core promoter: a key component in the regulation of gene expression.
Genes & development 2002;16(20):2583-92.
2002: Kadonaga James T
The DPE, a core promoter element for transcription by RNA polymerase II.
Experimental & molecular medicine 2002;34(4):259-64.
2002: Fyodorov Dmitry V; Kadonaga James T
Binding of Acf1 to DNA involves a WAC motif and is important for ACF-mediated chromatin assembly.
Molecular and cellular biology 2002;22(18):6344-53.
2002: Fyodorov Dmitry V; Kadonaga James T
Dynamics of ATP-dependent chromatin assembly by ACF.
Nature 2002;418(6900):897-900.
2002: Levenstein Mark E; Kadonaga James T
Biochemical analysis of chromatin containing recombinant Drosophila core histones.
The Journal of biological chemistry 2002;277(10):8749-54.
2001: Butler J E; Kadonaga J T
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs.
Genes & development 2001;15(19):2515-9.
2001: Tyler J K; Collins K A; Prasad-Sinha J; Amiott E; Bulger M; Harte P J; Kobayashi R; Kadonaga J T
Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors.
Molecular and cellular biology 2001;21(19):6574-84.
2001: Fyodorov D V; Kadonaga J T
The many faces of chromatin remodeling: SWItching beyond transcription.
Cell 2001;106(5):523-5.
2001: Manning E T; Ikehara T; Ito T; Kadonaga J T; Kraus W L
p300 forms a stable, template-committed complex with chromatin: role for the bromodomain.
Molecular and cellular biology 2001;21(12):3876-87.
2001: Huang X; Kadonaga J T
Biochemical analysis of transcriptional repression by Drosophila histone deacetylase 1.
The Journal of biological chemistry 2001;276(16):12497-500.
2000: Jiang W; Nordeen S K; Kadonaga J T
Transcriptional analysis of chromatin assembled with purified ACF and dNAP1 reveals that acetyl-CoA is required for preinitiation complex assembly.
The Journal of biological chemistry 2000;275(51):39819-22.
2000: Willy P J; Kobayashi R; Kadonaga J T
A basal transcription factor that activates or represses transcription.
Science (New York, N.Y.) 2000;290(5493):982-5.
2000: Kutach A K; Kadonaga J T
The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters.
Molecular and cellular biology 2000;20(13):4754-64.
1999: Tyler J K; Adams C R; Chen S R; Kobayashi R; Kamakaka R T; Kadonaga J T
The RCAF complex mediates chromatin assembly during DNA replication and repair.
Nature 1999;402(6761):555-60.
1999: Kraus W L; Manning E T; Kadonaga J T
Biochemical analysis of distinct activation functions in p300 that enhance transcription initiation with chromatin templates.
Molecular and cellular biology 1999;19(12):8123-35.
1999: Tyler J K; Kadonaga J T
The "dark side" of chromatin remodeling: repressive effects on transcription.
Cell 1999;99(5):443-6.
1999: Ito T; Levenstein M E; Fyodorov D V; Kutach A K; Kobayashi R; Kadonaga J T
ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly.
Genes & development 1999;13(12):1529-39.
1998: Pazin M J; Hermann J W; Kadonaga J T
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.
The Journal of biological chemistry 1998;273(51):34653-60.
1998: Näär A M; Beaurang P A; Robinson K M; Oliner J D; Avizonis D; Scheek S; Zwicker J; Kadonaga J T; Tjian R
Chromatin, TAFs, and a novel multiprotein coactivator are required for synergistic activation by Sp1 and SREBP-1a in vitro.
Genes & development 1998;12(19):3020-31.
1998: Robinson K M; Kadonaga J T
The use of chromatin templates to recreate transcriptional regulatory phenomena in vitro.
Biochimica et biophysica acta 1998;1378(1):M1-6.
1998: Blackwood E M; Kadonaga J T
Going the distance: a current view of enhancer action.
Science (New York, N.Y.) 1998;281(5373):60-3.
1998: Kadonaga J T
Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines.
Cell 1998;92(3):307-13.
1998: Kraus W L; Kadonaga J T
p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation.
Genes & development 1998;12(3):331-42.
1998: Burke T W; Willy P J; Kutach A K; Butler J E; Kadonaga J T
The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box.
Cold Spring Harbor symposia on quantitative biology 1998;63():75-82.
1997: Burke T W; Kadonaga J T
The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila.
Genes & development 1997;11(22):3020-31.
1997: Ito T; Tyler J K; Kadonaga J T
Chromatin assembly factors: a dual function in nucleosome formation and mobilization?
Genes to cells : devoted to molecular & cellular mechanisms 1997;2(10):593-600.
1997: Ito T; Bulger M; Pazin M J; Kobayashi R; Kadonaga J T
ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor.
Cell 1997;90(1):145-55.
1997: Ouhammouch M; Sayre M H; Kadonaga J T; Geiduschek E P
Activation of RNA polymerase II by topologically linked DNA-tracking proteins.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(13):6718-23.
1997: Pazin M J; Kadonaga J T
What's up and down with histone deacetylation and transcription?
Cell 1997;89(3):325-8.
1997: Pazin M J; Bhargava P; Geiduschek E P; Kadonaga J T
Nucleosome mobility and the maintenance of nucleosome positioning.
Science (New York, N.Y.) 1997;276(5313):809-12.
1997: Pazin M J; Kadonaga J T
SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions?
Cell 1997;88(6):737-40.
1996: Tyler J K; Bulger M; Kamakaka R T; Kobayashi R; Kadonaga J T
The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase-associated protein.
Molecular and cellular biology 1996;16(11):6149-59.
1996: Ito T; Tyler J K; Bulger M; Kobayashi R; Kadonaga J T
ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster.
The Journal of biological chemistry 1996;271(40):25041-8.
1996: Ito T; Bulger M; Kobayashi R; Kadonaga J T
Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays.
Molecular and cellular biology 1996;16(6):3112-24.
1996: Kamakaka R T; Bulger M; Kaufman P D; Stillman B; Kadonaga J T
Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1.
Molecular and cellular biology 1996;16(3):810-7.
1996: Burke T W; Kadonaga J T
Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters.
Genes & development 1996;10(6):711-24.
1996: Pazin M J; Sheridan P L; Cannon K; Cao Z; Keck J G; Kadonaga J T; Jones K A
NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro.
Genes & development 1996;10(1):37-49.
1995: Bulger M; Ito T; Kamakaka R T; Kadonaga J T
Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(25):11726-30.
1995: Sheridan P L; Sheline C T; Cannon K; Voz M L; Pazin M J; Kadonaga J T; Jones K A
Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro.
Genes & development 1995;9(17):2090-104.
1995: Paranjape S M; Krumm A; Kadonaga J T
HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation.
Genes & development 1995;9(16):1978-91.
1995: Frank D J; Tyree C M; George C P; Kadonaga J T
Structure and function of the small subunit of TFIIF (RAP30) from Drosophila melanogaster.
The Journal of biological chemistry 1995;270(11):6292-7.
1995: Lira-DeVito L M; Burke T W; Kadonaga J T
Structure of the genes encoding transcription factor IIB and TATA box-binding protein from Drosophila melanogaster.
Gene 1995;153(2):203-7.
1995: George C P; Lira-DeVito L M; Wampler S L; Kadonaga J T
A spectrum of mechanisms for the assembly of the RNA polymerase II transcription preinitiation complex.
Molecular and cellular biology 1995;15(2):1049-59.
1994: Pazin M J; Kamakaka R T; Kadonaga J T
ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates.
Science (New York, N.Y.) 1994;266(5193):2007-11.
1994: Kamakaka R T; Kaufman P D; Stillman B; Mitsis P G; Kadonaga J T
Simian virus 40 origin- and T-antigen-dependent DNA replication with Drosophila factors in vitro.
Molecular and cellular biology 1994;14(8):5114-22.
1994: Paranjape S M; Kamakaka R T; Kadonaga J T
Role of chromatin structure in the regulation of transcription by RNA polymerase II.
Annual review of biochemistry 1994;63():265-97.
1994: Kamakaka R T; Kadonaga J T
The soluble nuclear fraction, a highly efficient transcription extract from Drosophila embryos.
Methods in cell biology 1994;44():225-35.
1993: Kamakaka R T; Bulger M; Kadonaga J T
Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly.
Genes & development 1993;7(9):1779-95.
1993: Tyree C M; George C P; Lira-DeVito L M; Wampler S L; Dahmus M E; Zawel L; Kadonaga J T
Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II.
Genes & development 1993;7(7A):1254-65.
1993: Croston G E; Kadonaga J T
Role of chromatin structure in the regulation of transcription by RNA polymerase II.
Current opinion in cell biology 1993;5(3):417-23.
1993: Klucher K M; Sommer M; Kadonaga J T; Spector D H
In vivo and in vitro analysis of transcriptional activation mediated by the human cytomegalovirus major immediate-early proteins.
Molecular and cellular biology 1993;13(2):1238-50.
1993: Kamakaka R T; Kadonaga J T
Biochemical analysis of the role of chromatin structure in the regulation of transcription by RNA polymerase II.
Cold Spring Harbor symposia on quantitative biology 1993;58():205-12.
1992: Kerrigan L A; Kadonaga J T
Periodic binding of individual core histones to DNA: inadvertent purification of the core histone H2B as a putative enhancer-binding factor.
Nucleic acids research 1992;20(24):6673-80.
1992: Croston G E; Laybourn P J; Paranjape S M; Kadonaga J T
Mechanism of transcriptional antirepression by GAL4-VP16.
Genes & development 1992;6(12A):2270-81.
1992: Laybourn P J; Kadonaga J T
Threshold phenomena and long-distance activation of transcription by RNA polymerase II.
Science (New York, N.Y.) 1992;257(5077):1682-5.
1992: Wampler S L; Kadonaga J T
Functional analysis of Drosophila transcription factor IIB.
Genes & development 1992;6(8):1542-52.
1991: Laybourn P J; Kadonaga J T
Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II.
Science (New York, N.Y.) 1991;254(5029):238-45.
1991: Croston G E; Lira L M; Kadonaga J T
A general method for purification of H1 histones that are active for repression of basal RNA polymerase II transcription.
Protein expression and purification 1991;2(2-3):162-9.
1991: Kamakaka R T; Tyree C M; Kadonaga J T
Accurate and efficient RNA polymerase II transcription with a soluble nuclear fraction derived from Drosophila embryos.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(3):1024-8.
1991: Croston G E; Kerrigan L A; Lira L M; Marshak D R; Kadonaga J T
Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription.
Science (New York, N.Y.) 1991;251(4994):643-9.
1991: Kerrigan L A; Croston G E; Lira L M; Kadonaga J T
Sequence-specific transcriptional antirepression of the Drosophila Krüppel gene by the GAGA factor.
The Journal of biological chemistry 1991;266(1):574-82.
1990: Wampler S L; Tyree C M; Kadonaga J T
Fractionation of the general RNA polymerase II transcription factors from Drosophila embryos.
The Journal of biological chemistry 1990;265(34):21223-31.
1990: Kadonaga J T
Gene transcription: basal and regulated transcription by RNA polymerase II.
Current opinion in cell biology 1990;2(3):496-501.
1990: Kadonaga J T
Assembly and disassembly of the Drosophila RNA polymerase II complex during transcription.
The Journal of biological chemistry 1990;265(5):2624-31.

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