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Items: 1 to 50 of 135

1.

The RNA Polymerase II Core Promoter in Drosophila.

Vo Ngoc L, Kassavetis GA, Kadonaga JT.

Genetics. 2019 May;212(1):13-24. doi: 10.1534/genetics.119.302021.

PMID:
31053615
2.

Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes.

Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T.

PLoS One. 2019 Apr 18;14(4):e0215695. doi: 10.1371/journal.pone.0215695. eCollection 2019.

3.

Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog.

Wang W, Xu J, Limbo O, Fei J, Kassavetis GA, Chong J, Kadonaga JT, Russell P, Li B, Wang D.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6120-6129. doi: 10.1073/pnas.1818163116. Epub 2019 Mar 13.

PMID:
30867290
4.

NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes.

Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT.

Genes Dev. 2018 May 1;32(9-10):682-694. doi: 10.1101/gad.313973.118. Epub 2018 May 14.

5.

A simple and versatile system for the ATP-dependent assembly of chromatin.

Khuong MT, Fei J, Cruz-Becerra G, Kadonaga JT.

J Biol Chem. 2017 Nov 24;292(47):19478-19490. doi: 10.1074/jbc.M117.815365. Epub 2017 Oct 5.

6.

The punctilious RNA polymerase II core promoter.

Vo Ngoc L, Wang YL, Kassavetis GA, Kadonaga JT.

Genes Dev. 2017 Jul 1;31(13):1289-1301. doi: 10.1101/gad.303149.117. Review.

7.

The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters.

Vo Ngoc L, Cassidy CJ, Huang CY, Duttke SH, Kadonaga JT.

Genes Dev. 2017 Jan 1;31(1):6-11. doi: 10.1101/gad.293837.116. Epub 2017 Jan 20.

8.

Prenucleosomes and Active Chromatin.

Khuong MT, Fei J, Ishii H, Kadonaga JT.

Cold Spring Harb Symp Quant Biol. 2015;80:65-72. doi: 10.1101/sqb.2015.80.027300. Epub 2016 Jan 14. Review.

9.

The prenucleosome, a stable conformational isomer of the nucleosome.

Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT.

Genes Dev. 2015 Dec 15;29(24):2563-75. doi: 10.1101/gad.272633.115.

10.

Perspectives on Unidirectional versus Divergent Transcription.

Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U.

Mol Cell. 2015 Nov 5;60(3):348-9. doi: 10.1016/j.molcel.2015.10.014. No abstract available.

11.

MPE-seq, a new method for the genome-wide analysis of chromatin structure.

Ishii H, Kadonaga JT, Ren B.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3457-65. doi: 10.1073/pnas.1424804112. Epub 2015 Jun 15.

12.

Human promoters are intrinsically directional.

Duttke SHC, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U.

Mol Cell. 2015 Feb 19;57(4):674-684. doi: 10.1016/j.molcel.2014.12.029. Epub 2015 Jan 29.

13.

Regulation of the Rhp26ERCC6/CSB chromatin remodeler by a novel conserved leucine latch motif.

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.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18566-71. doi: 10.1073/pnas.1420227112. Epub 2014 Dec 15.

14.

TRF2 and the evolution of the bilateria.

Duttke SH, Doolittle RF, Wang YL, Kadonaga JT.

Genes Dev. 2014 Oct 1;28(19):2071-6. doi: 10.1101/gad.250563.114.

15.

TRF2, but not TBP, mediates the transcription of ribosomal protein genes.

Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT.

Genes Dev. 2014 Jul 15;28(14):1550-5. doi: 10.1101/gad.245662.114. Epub 2014 Jun 23.

16.

The annealing helicase and branch migration activities of Drosophila HARP.

Kassavetis GA, Kadonaga JT.

PLoS One. 2014 May 27;9(5):e98173. doi: 10.1371/journal.pone.0098173. eCollection 2014.

17.

ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling.

Torigoe SE, Patel A, Khuong MT, Bowman GD, Kadonaga JT.

Elife. 2013 Aug 20;2:e00863. doi: 10.7554/eLife.00863.

18.

Biochemical analysis of histone deacetylase-independent transcriptional repression by MeCP2.

Theisen JW, Gucwa JS, Yusufzai T, Khuong MT, Kadonaga JT.

J Biol Chem. 2013 Mar 8;288(10):7096-104. doi: 10.1074/jbc.M112.438697. Epub 2013 Jan 24.

19.

Human TFIID binds to core promoter DNA in a reorganized structural state.

Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E.

Cell. 2013 Jan 17;152(1-2):120-31. doi: 10.1016/j.cell.2012.12.005.

20.

Perspectives on the RNA polymerase II core promoter.

Kadonaga JT.

Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb;1(1):40-51. doi: 10.1002/wdev.21. Epub 2011 Dec 6. Review.

21.

Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF.

Torigoe SE, Urwin DL, Ishii H, Smith DE, Kadonaga JT.

Mol Cell. 2011 Aug 19;43(4):638-48. doi: 10.1016/j.molcel.2011.07.017.

22.

Branching out with DNA helicases.

Yusufzai T, Kadonaga JT.

Curr Opin Genet Dev. 2011 Apr;21(2):214-8. doi: 10.1016/j.gde.2011.01.019. Epub 2011 Feb 15. Review.

23.

Annealing helicase 2 (AH2), a DNA-rewinding motor with an HNH motif.

Yusufzai T, Kadonaga JT.

Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):20970-3. doi: 10.1073/pnas.1011196107. Epub 2010 Nov 15.

24.

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery.

Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga JT.

Genes Dev. 2010 Sep 15;24(18):2013-8. doi: 10.1101/gad.1951110. Epub 2010 Aug 27.

25.

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2010 Aug;17(8):920-3. No abstract available.

26.

Three key subregions contribute to the function of the downstream RNA polymerase II core promoter.

Theisen JW, Lim CY, Kadonaga JT.

Mol Cell Biol. 2010 Jul;30(14):3471-9. doi: 10.1128/MCB.00053-10. Epub 2010 May 10.

27.

The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA.

Yusufzai T, Kong X, Yokomori K, Kadonaga JT.

Genes Dev. 2009 Oct 15;23(20):2400-4. doi: 10.1101/gad.1831509. Epub 2009 Sep 30.

28.

Regulation of gene expression via the core promoter and the basal transcriptional machinery.

Juven-Gershon T, Kadonaga JT.

Dev Biol. 2010 Mar 15;339(2):225-9. doi: 10.1016/j.ydbio.2009.08.009. Epub 2009 Aug 13. Review.

29.

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20.

30.

HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility.

Rattner BP, Yusufzai T, Kadonaga JT.

Mol Cell. 2009 Jun 12;34(5):620-6. doi: 10.1016/j.molcel.2009.04.014.

31.

HARP is an ATP-driven annealing helicase.

Yusufzai T, Kadonaga JT.

Science. 2008 Oct 31;322(5902):748-50. doi: 10.1126/science.1161233.

32.

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor.

Juven-Gershon T, Hsu JY, Kadonaga JT.

Genes Dev. 2008 Oct 15;22(20):2823-30. doi: 10.1101/gad.1698108.

33.

TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.

Hsu JY, Juven-Gershon T, Marr MT 2nd, Wright KJ, Tjian R, Kadonaga JT.

Genes Dev. 2008 Sep 1;22(17):2353-8. doi: 10.1101/gad.1681808. Epub 2008 Aug 14.

34.

Tools for neuroanatomy and neurogenetics in Drosophila.

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.

Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9715-20. doi: 10.1073/pnas.0803697105. Epub 2008 Jul 9.

35.

The RNA polymerase II core promoter - the gateway to transcription.

Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT.

Curr Opin Cell Biol. 2008 Jun;20(3):253-9. doi: 10.1016/j.ceb.2008.03.003. Epub 2008 Apr 22. Review.

36.

Purification of sequence-specific DNA-binding proteins by affinity chromatography.

Kerrigan LA, Kadonaga JT.

Curr Protoc Protein Sci. 2001 May;Chapter 9:Unit 9.6. doi: 10.1002/0471140864.ps0906s11.

PMID:
18429215
37.

Purification of sequence-specific DNA-binding proteins by affinity chromatography.

Kerrigan LA, Kadonaga JT.

Curr Protoc Mol Biol. 2001 May;Chapter 12:Unit 12.10. doi: 10.1002/0471142727.mb1210s24.

PMID:
18265082
38.

CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo.

Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga JT, Lusser A, Fyodorov DV.

Science. 2007 Aug 24;317(5841):1087-90.

39.

Rational design of a super core promoter that enhances gene expression.

Juven-Gershon T, Cheng S, Kadonaga JT.

Nat Methods. 2006 Nov;3(11):917-22.

PMID:
17124735
40.

Perspectives on the RNA polymerase II core promoter.

Juven-Gershon T, Hsu JY, Kadonaga JT.

Biochem Soc Trans. 2006 Dec;34(Pt 6):1047-50.

PMID:
17073747
41.

Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300.

Santoso B, Kadonaga JT.

Nat Struct Mol Biol. 2006 Feb;13(2):131-9. Epub 2006 Jan 15.

PMID:
16415879
42.

Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation.

Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen'ev MB, Kadonaga JT, Georgieva SG, Tora L.

Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18087-92. Epub 2005 Dec 5.

43.

Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF.

Gemmen GJ, Sim R, Haushalter KA, Ke PC, Kadonaga JT, Smith DE.

J Mol Biol. 2005 Aug 5;351(1):89-99.

PMID:
16002089
44.

Strategies for the reconstitution of chromatin.

Lusser A, Kadonaga JT.

Nat Methods. 2004 Oct;1(1):19-26. Review.

PMID:
15789029
45.

Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly.

Lusser A, Urwin DL, Kadonaga JT.

Nat Struct Mol Biol. 2005 Feb;12(2):160-6. Epub 2005 Jan 9.

PMID:
15643425
46.

The MTE, a new core promoter element for transcription by RNA polymerase II.

Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT.

Genes Dev. 2004 Jul 1;18(13):1606-17.

47.

A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing.

Alexiadis V, Lusser A, Kadonaga JT.

J Biol Chem. 2004 Jun 25;279(26):27824-9. Epub 2004 Apr 22.

48.

Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo.

Fyodorov DV, Blower MD, Karpen GH, Kadonaga JT.

Genes Dev. 2004 Jan 15;18(2):170-83.

49.
50.

Chromatin assembly in vitro with purified recombinant ACF and NAP-1.

Fyodorov DV, Kadonaga JT.

Methods Enzymol. 2003;371:499-515. No abstract available.

PMID:
14712724

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