Assembly of the transcription machinery: Ordered and stable, random and dynamic, or both?

Chromosoma

Volumn 120, Issue 6, 2011, Pages 533-545

  Stasevich, Timothy J ^a   McNally, James G ^b  

^a OSAKA UNIVERSITY   (Japan)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; RNA POLYMERASE II; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IIA; TRANSCRIPTION FACTOR IIB; TRANSCRIPTION FACTOR IID; TRANSCRIPTION FACTOR IIE; TRANSCRIPTION FACTOR IIF; TRANSCRIPTION FACTOR IIH; UNCLASSIFIED DRUG;

BIOCHEMISTRY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; EXPERIMENTAL MODEL; FLUORESCENCE MICROSCOPY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; GENE ACTIVATION; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; REVIEW; SURFACE PLASMON RESONANCE; SYSTEMATIC ERROR;

ANIMALS; DNA; DNA-DIRECTED RNA POLYMERASES; HUMANS; KINETICS; MULTIPROTEIN COMPLEXES; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 82355190137     PISSN: 00095915     EISSN: 14320886     Source Type: Journal    
DOI: 10.1007/s00412-011-0340-y     Document Type: Review

References (97)

1. T Agalioti S Lomvardas B Parekh J Yie T Maniatis D Thanos 2000 Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter Cell 103 667 678 11106736 1:CAS:528:DC%2BD3cXot1Gmsr8%3D 10.1016/S0092-8674(00)00169-0
2. DT Auble KE Hansen CG Mueller WS Lane J Thorner S Hahn 1994 Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism Genes Dev 8 1920 1934 7958867 1:CAS:528:DyaK2cXmt1ems78%3D 10.1101/gad.8.16.1920 (Pubitemid 24273892)
3. AJ Bonham T Neumann M Tirrell NO Reich 2009 Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays Nucleic Acids Res 37 e94-e94 10.1093/nar/gkp424
4. D Bosisio I Marazzi A Agresti N Shimizu ME Bianchi G Natoli 2006 A hyper-dynamic equilibrium between promoter-bound and nucleoplasmic dimers controls NF-κB-dependent gene activity EMBO J 25 798 810 16467852 1:CAS:528:DC%2BD28Xhs1ersb4%3D 10.1038/sj.emboj.7600977 (Pubitemid 43292441)
5. S Buratowski 1994 The basics of basal transcription by RNA polymerase II Cell 77 1 3 8156586 1:CAS:528:DyaK2cXkslKhtrY%3D 10.1016/0092-8674(94)90226-7 (Pubitemid 24184679)
6. S Buratowski 2000 Snapshots of RNA polymerase II transcription initiation Curr Opin Cell Biol 12 320 325 10801469 1:CAS:528:DC%2BD3cXjsl2msbk%3D 10.1016/S0955-0674(00)00095-8 (Pubitemid 30265061)
7. DA Bushnell C Bamdad RD Kornberg 1996 A minimal set of RNA polymerase II transcription protein interactions J Biol Chem 271 20170 20174 8702741 1:CAS:528:DyaK28XltVKrt7c%3D 10.1074/jbc.271.36.21842 (Pubitemid 26303804)
8. F Catez T Ueda M Bustin 2006 Determinants of histone H1 mobility and chromatin binding in living cells Nat Struct Mol Biol 13 305 310 16715048 1:CAS:528:DC%2BD28Xjs1Ort7w%3D 10.1038/nsmb1077 (Pubitemid 43873500)
9. D Chen CS Hinkley RW Henry S Huang 2002 TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes Mol Biol Cell 13 276 284 11809839 1:CAS:528:DC%2BD38XnvFCiuw%3D%3D 10.1091/mbc.01-10-0523 (Pubitemid 34106075)
10. GA Collins WP Tansey 2006 The proteasome: a utility tool for transcription? Curr Opin Genet Dev 16 197 202 16503126 1:CAS:528: DC%2BD28Xis1eht7k%3D 10.1016/j.gde.2006.02.009 (Pubitemid 43376068)
11. RC Conaway JW Conaway 1993 General initiation factors for RNA polymerase II Annu Rev Biochem 62 161 190 8352588 1:CAS:528:DyaK3sXltV2qs7w%3D 10.1146/annurev.bi.62.070193.001113 (Pubitemid 23237869)
12. Cook PR (2001) Principles of nuclear structure and function, 1st edn. Wiley-Liss, New York
13. JA D'Alessio KJ Wright R Tjian 2009 Shifting players and paradigms in cell-specific transcription Mol Cell 36 924 931 20064459 10.1016/j.molcel.2009. 12.011
14. X Darzacq Y Shav-Tal V de Turris Y Brody SM Shenoy RD Phair RH Singer 2007 In vivo dynamics of RNA polymerase II transcription Nat Struct Mol Biol 14 796 806 17676063 1:CAS:528:DC%2BD2sXpvFKlu7k%3D 10.1038/nsmb1280 (Pubitemid 47373828)
15. X Darzacq J Yao DR Larson SZ Causse L Bosanac V de Turris VM Ruda T Lionnet D Zenklusen B Guglielmi R Tjian RH Singer 2009 Imaging transcription in living cells Annu Rev Biophys 38 173 196 19416065 1:CAS:528:DC%2BD1MXntlentL0%3D 10.1146/annurev.biophys.050708.133728
16. A Daulny F Geng M Muratani JM Geisinger SE Salghetti WP Tansey 2008 Modulation of RNA polymerase II subunit composition by ubiquitylation Proc Natl Acad Sci USA 105 19649 19654 19064926 1:CAS:528:DC%2BD1cXhsFCltrzL 10.1073/pnas.0809372105
17. P de Graaf F Mousson B Geverts E Scheer L Tora AB Houtsmuller HTM Timmers 2010 Chromatin interaction of TATA-binding protein is dynamically regulated in human cells J Cell Sci 123 2663 2671 20627952 10.1242/jcs.064097
18. W Deng SGE Roberts 2007 TFIIB and the regulation of transcription by RNA polymerase II Chromosoma 116 417 429 17593382 1:CAS:528:DC%2BD2sXhtVOit7jI 10.1007/s00412-007-0113-9 (Pubitemid 47456910)
19. DC Dezwaan BC Freeman 2008 HSP90: the Rosetta stone for cellular protein dynamics? Cell Cycle 7 1006 1012 18414022 1:CAS:528:DC%2BD1cXnvVSrsLg%3D 10.4161/cc.7.8.5723 (Pubitemid 351679833)
20. C Dinant MS Luijsterburg T Höfer G von Bornstaedt W Vermeulen AB Houtsmuller R van Driel 2009 Assembly of multiprotein complexes that control genome function J Cell Biol 185 21 26 19332890 1:CAS:528:DC%2BD1MXksFWrtrY%3D 10.1083/jcb.200811080
21. MR D'Orsogna T Chou 2005 First passage and cooperativity of queuing kinetics Phys Rev Lett 95 170603 16383812 10.1103/PhysRevLett.95.170603 (Pubitemid 41777344)
22. M Dundr U Hoffmann-Rohrer Q Hu I Grummt LI Rothblum RD Phair T Misteli 2002 A kinetic framework for a mammalian RNA polymerase in vivo Science 298 1623 1626 12446911 1:CAS:528:DC%2BD38Xosl2kuro%3D 10.1126/science.1076164 (Pubitemid 35387201)
23. C Elbi DA Walker G Romero WP Sullivan DO Toft GL Hager DB DeFranco 2004 Molecular chaperones function as steroid receptor nuclear mobility factors PNAS 101 2876 2881 14978266 1:CAS:528:DC%2BD2cXitlWhsL4%3D 10.1073/pnas.0400116101 (Pubitemid 38327704)
24. C Evrin P Clarke J Zech R Lurz J Sun S Uhle H Li B Stillman C Speck 2009 A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication Proc Natl Acad Sci USA 106 20240 20245 19910535 1:CAS:528:DC%2BC3cXjtFSktQ%3D%3D 10.1073/pnas.0911500106
25. TM Fletcher N Xiao G Mautino CT Baumann R Wolford BS Warren GL Hager 2002 ATP-dependent mobilization of the glucocorticoid receptor during chromatin remodeling Mol Cell Biol 22 3255 3263 11971959 1:CAS:528:DC%2BD38XjtlWgsL8%3D 10.1128/MCB.22.10.3255-3263.2002 (Pubitemid 34460550)
26. BC Freeman KR Yamamoto 2002 Disassembly of transcriptional regulatory complexes by molecular chaperones Science 296 2232 2235 12077419 1:CAS:528:DC%2BD38XkvFGht7w%3D 10.1126/science.1073051 (Pubitemid 34680310)
27. G Giglia-Mari AF Theil P-O Mari S Mourgues J Nonnekens LO Andrieux J de Wit C Miquel N Wijgers A Maas M Fousteri JHJ Hoeijmakers W Vermeulen 2009 Differentiation driven changes in the dynamic organization of basal transcription initiation PLoS Biol 7 e1000220 19841728 10.1371/journal.pbio. 1000220
28. SA Gorski SK Snyder S John I Grummt T Misteli 2008 Modulation of RNA polymerase assembly dynamics in transcriptional regulation Mol Cell 30 486 497 18498750 1:CAS:528:DC%2BD1cXmslOiurw%3D 10.1016/j.molcel.2008.04.021 (Pubitemid 351672375)
29. M Guermah J Kim RG Roeder 2009 Transcription of in vitro assembled chromatin templates in a highly purified RNA polymerase II system Methods 48 353 360 19272450 1:CAS:528:DC%2BD1MXpt1Kisr8%3D 10.1016/j.ymeth.2009.02.022
30. GL Hager C Elbi TA Johnson T Voss AK Nagaich RL Schiltz Y Qiu S John 2006 Chromatin dynamics and the evolution of alternate promoter states Chromosome Res 14 107 116 16506100 1:CAS:528:DC%2BD28XhvVyqtLk%3D 10.1007/s10577-006-1030-0
31. GL Hager JG McNally T Misteli 2009 Transcription dynamics Mol Cell 35 741 753 19782025 1:CAS:528:DC%2BD1MXhsVChsr%2FJ 10.1016/j.molcel.2009.09.005
32. S Hahn 2004 Structure and mechanism of the RNA polymerase II transcription machinery Nat Struct Mol Biol 11 394 403 15114340 1:CAS:528:DC%2BD2cXjsVCqsL0%3D 10.1038/nsmb763
33. AH Hassan P Prochasson KE Neely SC Galasinski M Chandy MJ Carrozza JL Workman 2002 Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes Cell 111 369 379 12419247 1:CAS:528:DC%2BD38XovVaku7w%3D 10.1016/S0092-8674(02)01005-X (Pubitemid 35345152)
34. Y Hayashi-Takanaka K Yamagata N Nozaki H Kimura 2009 Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase J Cell Biol 187 781 790 19995936 1:CAS:528:DC%2BD1MXhsF2qtbrN 10.1083/jcb.200904137
35. P Hemmerich L Schmiedeberg S Diekmann 2010 Dynamic as well as stable protein interactions contribute to genome function and maintenance Chromosome Res 19 131 151 10.1007/s10577-010-9161-8
36. D Hoogstraten AL Nigg H Heath LHF Mullenders R van Driel JHJ Hoeijmakers W Vermeulen AB Houtsmuller 2002 Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo Mol Cell 10 1163 1174 12453423 1:CAS:528:DC%2BD38Xptl2ksbY%3D 10.1016/S1097-2765(02)00709-8 (Pubitemid 35453833)
37. BC Hoopes JF LeBlanc DK Hawley 1992 Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway J Biol Chem 267 11539 11547 1597482 1:CAS:528:DyaK38XksVWru7o%3D
38. JJ Hopfield 1974 Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity Proc Natl Acad Sci USA 71 4135 4139 4530290 1:CAS:528:DyaE2MXpsVehsg%3D%3D 10.1073/pnas.71.10.4135
39. AA Hoskins LJ Friedman SS Gallagher DJ Crawford EG Anderson R Wombacher N Ramirez VW Cornish J Gelles MJ Moore 2011 Ordered and dynamic assembly of single spliceosomes Science 331 1289 1295 21393538 1:CAS:528: DC%2BC3MXivVWkt7w%3D 10.1126/science.1198830
40. J Iwahara GM Clore 2006 Detecting transient intermediates in macromolecular binding by paramagnetic NMR Nature 440 1227 1230 16642002 1:CAS:528:DC%2BD28XjvVGltLc%3D 10.1038/nature04673
41. TA Johnson C Elbi BS Parekh GL Hager S John 2008 Chromatin remodeling complexes interact dynamically with a glucocorticoid receptor-regulated promoter Mol Biol Cell 19 3308 3322 18508913 1:CAS:528:DC%2BD1cXpvV2hsrk%3D 10.1091/mbc.E08-02-0123
42. T Juven-Gershon J-Y Hsu JW Theisen JT Kadonaga 2008 The RNA polymerase II core promoter-the gateway to transcription Curr Opin Cell Biol 20 253 259 18436437 1:CAS:528:DC%2BD1cXmvV2lsr4%3D 10.1016/j.ceb.2008.03.003
43. JT Kadonaga 1990 Assembly and disassembly of the Drosophila RNA polymerase II complex during transcription J Biol Chem 265 2624 2631 1689291 1:CAS:528:DyaK3cXhsFChur4%3D
44. TE Kaiser RV Intine M Dundr 2008 De novo formation of a subnuclear body Science 322 1713 1717 18948503 1:CAS:528:DC%2BD1cXhsVOgtbvL 10.1126/science. 1165216
45. TS Karpova TY Chen BL Sprague JG McNally 2004 Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller EMBO Rep 5 1064 1070 15514679 1:CAS:528:DC%2BD2cXptFems7o%3D 10.1038/sj.embor.7400281 (Pubitemid 39600205)
46. TS Karpova MJ Kim C Spriet K Nalley TJ Stasevich Z Kherrouche L Heliot JG McNally 2008 Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter Science 319 466 469 18218898 1:CAS:528: DC%2BD1cXovFGiug%3D%3D 10.1126/science.1150559 (Pubitemid 351160580)
47. H Kimura Y Tao RG Roeder PR Cook 1999 Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure Mol Cell Biol 19 5383 5392 10409729 1:CAS:528:DyaK1MXkvVKjs70%3D (Pubitemid 29339897)
48. H Kimura K Sugaya PR Cook 2002 The transcription cycle of RNA polymerase II in living cells J Cell Biol 159 777 782 12473686 1:CAS:528: DC%2BD38XpsFCqtbg%3D 10.1083/jcb.200206019 (Pubitemid 36008360)
49. RD Kornberg 2007 The molecular basis of eukaryotic transcription Proc Natl Acad Sci USA 104 12955 12961 17670940 1:CAS:528:DC%2BD2sXpt1KrtL8%3D 10.1073/pnas.0704138104 (Pubitemid 351737575)
50. MA Kuipers TJ Stasevich T Sasaki KA Wilson KL Hazelwood JG McNally MW Davidson DM Gilbert 2011 Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload J Cell Biol 192 29 41 21220507 1:CAS:528:DC%2BC3MXnsl2hsQ%3D%3D 10.1083/jcb.201007111
51. B Lemon R Tjian 2000 Orchestrated response: a symphony of transcription factors for gene control Genes Dev 14 2551 2569 11040209 1:CAS:528: DC%2BD3cXnslGrurc%3D 10.1101/gad.831000
52. G Li R Margueron G Hu D Stokes Y-H Wang D Reinberg 2010 Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo Mol Cell 38 41 53 20385088 10.1016/j.molcel.2010.01.042
53. BA Lieberman SK Nordeen 1997 DNA intersegment transfer, how steroid receptors search for a target site J Biol Chem 272 1061 1068 8995403 1:CAS:528:DyaK2sXmtFGltQ%3D%3D 10.1074/jbc.272.2.1061 (Pubitemid 27034599)
54. J Linnell R Mott S Field DP Kwiatkowski J Ragoussis IA Udalova 2004 Quantitative high-throughput analysis of transcription factor binding specificities Nucleic Acids Res 32 e44-e44 10.1093/nar/gnh042
55. MS Luijsterburg G von Bornstaedt AM Gourdin AZ Politi MJ Moné DO Warmerdam J Goedhart W Vermeulen R van Driel T Höfer 2010 Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair J Cell Biol 189 445 463 20439997 1:CAS:528:DC%2BC3cXlvFyhtb4%3D 10.1083/jcb.200909175
56. JL Manley A Fire A Cano PA Sharp ML Gefter 1980 DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract Proc Natl Acad Sci USA 77 3855 3859 6933441 1:CAS:528:DyaL3cXlvVWhsL0%3D 10.1073/pnas.77.7. 3855 (Pubitemid 10015480)
57. BR Martin BNG Giepmans SR Adams RY Tsien 2005 Mammalian cell-based optimization of the biarsenical-binding tetracysteine motif for improved fluorescence and affinity Nat Biotechnol 23 1308 1314 16155565 1:CAS:528:DC%2BD2MXhtVOhu7jL 10.1038/nbt1136 (Pubitemid 41486860)
58. AJ McNairn Y Okuno T Misteli DM Gilbert 2005 Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle Exp Cell Res 308 345 356 15950218 1:CAS:528:DC%2BD2MXmvVCht7Y%3D 10.1016/j.yexcr.2005.05.009
59. S Mizushima M Nomura 1970 Assembly mapping of 30S ribosomal proteins from E. coli Nature 226 1214 4912319 1:CAS:528:DyaE3cXkvVeqt7s%3D 10.1038/2261214a0
60. D Mu DS Hsu A Sancar 1996 Reaction mechanism of human DNA repair excision nuclease J Biol Chem 271 8285 8294 8626523 1:CAS:528:DyaK28XitFarur4%3D 10.1074/jbc.271.32.19451 (Pubitemid 26271618)
61. F Mueller P Wach JG McNally 2008 Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching Biophys J 94 3323 3339 18199661 1:CAS:528:DC%2BD1cXkt1Cgsr4%3D 10.1529/biophysj.107.123182
62. F Mueller D Mazza TJ Stasevich JG McNally 2010 FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? Curr Opin Cell Biol 22 403 411 20413286 1:CAS:528:DC%2BC3cXntVynsrc%3D 10.1016/j.ceb.2010.03.002
63. F Muller L Tora 2004 The multicoloured world of promoter recognition complexes EMBO J 23 2 8 14685269 10.1038/sj.emboj.7600027 (Pubitemid 38165742)
64. KPN Murthy KW Kehr 1989 Mean first-passage time of random walks on a random lattice Phys Rev A 40 2082 9902366 10.1103/PhysRevA.40.2082
65. KPN Murthy KW Kehr 1990 Erratum: mean first-passage time of random walks on a random lattice Phys Rev A 41 1160 9903202 10.1103/PhysRevA.41.1160
66. AK Nagaich DA Walker R Wolford GL Hager 2004 Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling Mol Cell 14 163 174 15099516 1:CAS:528:DC%2BD2cXjvVyisLc%3D 10.1016/S1097-2765(04)00178- 9 (Pubitemid 38519068)
67. K Nalley SA Johnston T Kodadek 2006 Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo Nature 442 1054 1057 16929306 1:CAS:528:DC%2BD28XovVyhtbk%3D 10.1038/nature05067 (Pubitemid 44330264)
68. K Nalley SA Johnston T Kodadek 2009 Nalley et al. reply Nature 461 E8 1:CAS:528:DC%2BD1MXht1CisLfM 10.1038/nature08407
69. T Perlmann P Eriksson O Wrange 1990 Quantitative analysis of the glucocorticoid receptor-DNA interaction at the mouse mammary tumor virus glucocorticoid response element J Biol Chem 265 17222 17229 2170368 1:CAS:528:DyaK3cXlvVGlsLc%3D
70. IU Rafalska-Metcalf SL Powers LM Joo G LeRoy SM Janicki 2010 Single cell analysis of transcriptional activation dynamics PLoS One 5 e10272 20422051 10.1371/journal.pone.0010272
71. DN Roberts AJ Stewart JT Huff BR Cairns 2003 The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships Proc Natl Acad Sci USA 100 14695 14700 14634212 1:CAS:528:DC%2BD3sXpvFaqs74%3D 10.1073/pnas.2435566100 (Pubitemid 37517953)
72. RG Roeder 1996 The role of general initiation factors in transcription by RNA polymerase II Trends Biochem Sci 21 327 335 8870495 1:CAS:528: DyaK28Xlsl2ntbc%3D (Pubitemid 26298211)
73. B Santoso JT Kadonaga 2006 Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300 Nat Struct Mol Biol 13 131 139 16415879 1:CAS:528:DC%2BD28XhtFajsbg%3D 10.1038/nsmb1048 (Pubitemid 43214716)
74. DA Schneider M Nomura 2004 RNA polymerase I remains intact without subunit exchange through multiple rounds of transcription in Saccharomyces cerevisiae Proc Natl Acad Sci USA 101 15112 15117 15477604 1:CAS:528: DC%2BD2cXpsVSgs78%3D 10.1073/pnas.0406746101 (Pubitemid 39391727)
75. T Seki JFX Diffley 2000 Stepwise assembly of initiation proteins at budding yeast replication origins in vitro Proc Natl Acad Sci USA 97 14115 14120 11121019 1:CAS:528:DC%2BD3MXitVChuw%3D%3D 10.1073/pnas.97.26.14115 (Pubitemid 32016539)
76. JS Shumaker-Parry R Aebersold CT Campbell 2004 Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy Anal Chem 76 2071 2082 15053673 1:CAS:528:DC%2BD2cXhslCqtL0%3D 10.1021/ac035159j (Pubitemid 38451529)
77. JP Siebrasse U Kubitscheck 2009 Single molecule tracking for studying nucleocytoplasmic transport and intranuclear dynamics Methods Mol Biol 464 343 361 18951194 10.1007/978-1-60327-461-6-19
78. TW Sikorski S Buratowski 2009 The basal initiation machinery: beyond the general transcription factors Curr Opin Cell Biol 21 344 351 19411170 1:CAS:528:DC%2BD1MXmvFGgu7g%3D 10.1016/j.ceb.2009.03.006
79. D Sinnecker P Voigt N Hellwig M Schaefer 2005 Reversible photobleaching of enhanced green fluorescent proteins Biochemistry 44 7085 7094 15865453 1:CAS:528:DC%2BD2MXjtFGit7s%3D 10.1021/bi047881x (Pubitemid 40632426)
80. DR Sisan D Yarar CM Waterman JS Urbach 2010 Event ordering in live-cell imaging determined from temporal cross-correlation asymmetry Biophys J 98 2432 2441 20513386 1:CAS:528:DC%2BC3cXpsVOjtrc%3D 10.1016/j.bpj.2010.02.041
81. RO Sprouse TS Karpova F Mueller A Dasgupta JG McNally DT Auble 2008 Regulation of TATA-binding protein dynamics in living yeast cells Proc Natl Acad Sci USA 105 13304 13308 18765812 1:CAS:528:DC%2BD1cXhtFChs7zP 10.1073/pnas.0801901105
82. TJ Stasevich F Mueller A Michelman-Ribeiro T Rosales JR Knutson JG McNally 2010 Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates Biophys J 99 3093 3101 21044608 1:CAS:528:DC%2BC3cXhtlKkur3M 10.1016/j.bpj.2010.08.059
83. DA Stavreva WG Muller GL Hager CL Smith JG McNally 2004 Rapid glucocorticoid receptor exchange at a promoter is coupled to transcription and regulated by chaperones and proteasomes Mol Cell Biol 24 2682 2697 15024059 1:CAS:528:DC%2BD2cXis1emsL0%3D 10.1128/MCB.24.7.2682-2697.2004 (Pubitemid 38381261)
84. M-H Sung L Salvatore R De Lorenzi A Indrawan M Pasparakis GL Hager ME Bianchi A Agresti 2009 Sustained oscillations of NF-κB produce distinct genome scanning and gene expression profiles PLoS One 4 e7163 19787057 10.1371/journal.pone.0007163
85. MWT Talkington G Siuzdak JR Williamson 2005 An assembly landscape for the 30S ribosomal subunit Nature 438 628 632 16319883 1:CAS:528: DC%2BD2MXht1Gqs7%2FF 10.1038/nature04261 (Pubitemid 41740567)
86. M Tokunaga N Imamoto K Sakata-Sogawa 2008 Highly inclined thin illumination enables clear single-molecule imaging in cells Nat Methods 5 159 161 18176568 1:CAS:528:DC%2BD1cXhsV2ks7c%3D 10.1038/nmeth1171 (Pubitemid 351181742)
87. C Uttamapinant KA White H Baruah S Thompson M Fernández- Suárez S Puthenveetil AY Ting 2010 A fluorophore ligase for site-specific protein labeling inside living cells Proc Natl Acad Sci USA 107 10914 10919 20534555 1:CAS:528:DC%2BC3cXotVKqu7o%3D 10.1073/pnas.0914067107
88. FJ van Werven HAAM van Teeffelen FCP Holstege HTM Timmers 2009 Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome Nat Struct Mol Biol 16 1043 1048 19767748 10.1038/nsmb.1674
89. S Weidtkamp-Peters T Lenser D Negorev N Gerstner TG Hofmann G Schwanitz C Hoischen G Maul P Dittrich P Hemmerich 2008 Dynamics of component exchange at PML nuclear bodies J Cell Sci 121 2731 2743 18664490 1:CAS:528: DC%2BD1cXhtFKhu7vP 10.1242/jcs.031922
90. PA Weil DS Luse J Segall RG Roeder 1979 Selective and accurate initiation of transcription at the Ad2 major late promotor in a soluble system dependent on purified RNA polymerase II and DNA Cell 18 469 484 498279 1:CAS:528:DyaL3cXhslGi 10.1016/0092-8674(79)90065-5 (Pubitemid 10248370)
91. G Xouri A Squire M Dimaki B Geverts PJ Verveer S Taraviras H Nishitani AB Houtsmuller PIH Bastiaens Z Lygerou 2007 Cdt1 associates dynamically with chromatin throughout G1 and recruits Geminin onto chromatin EMBO J 26 1303 1314 17318181 1:CAS:528:DC%2BD2sXisVKqs7w%3D 10.1038/sj.emboj.7601597 (Pubitemid 46398717)
92. J Yao KM Munson WW Webb JT Lis 2006 Dynamics of heat shock factor association with native gene loci in living cells Nature 442 1050 1053 16929308 1:CAS:528:DC%2BD28XovVyhtbs%3D 10.1038/nature05025 (Pubitemid 44330263)
93. J Yao MB Ardehali CJ Fecko WW Webb JT Lis 2007 Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation Mol Cell 28 978 990 18158896 1:CAS:528:DC%2BD1cXksFyisw%3D%3D 10.1016/j.molcel.2007.10. 017 (Pubitemid 350297022)
94. D Yean J Gralla 1997 Transcription reinitiation rate: a special role for the TATA box Mol Cell Biol 17 3809 3816 9199314 1:CAS:528:DyaK2sXktFOntro%3D (Pubitemid 27281855)
95. N Yudkovsky JA Ranish S Hahn 2000 A transcription reinitiation intermediate that is stabilized by activator Nature 408 225 229 11089979 1:CAS:528:DC%2BD3cXotFGltL4%3D 10.1038/35041603
96. L Zawel KP Kumar D Reinberg 1995 Recycling of the general transcription factors during RNA polymerase II transcription Genes Dev 9 1479 1490 7601352 1:CAS:528:DyaK2MXms1equr8%3D 10.1101/gad.9.12.1479
97. KL Zobeck MS Buckley WR Zipfel JT Lis 2010 Recruitment timing and dynamics of transcription factors at the Hsp70 loci in living cells Mol Cell 40 965 975 21172661 1:CAS:528:DC%2BC3cXhsF2itr7O 10.1016/j.molcel.2010.11.022