ATP-dependent chromatin remodeling

Advances in Experimental Medicine and Biology

Volumn 767, Issue , 2013, Pages 263-295

  Yodh, Jaya ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; CHROMATIN REMODELLING COMPLEX; DOUBLE STRANDED DNA; EPITOPE; MOLECULAR MOTOR; MULTIENZYME COMPLEX; UNCLASSIFIED DRUG; DIMER; HELICASE; HISTONE; NUCLEOSOME; TRANSCRIPTION FACTOR;

ARTICLE; CATALYSIS; CELL NUCLEUS; CELL STRUCTURE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DIMERIZATION; DNA CROSS LINKING; DNA HISTONE INTERACTION; DNA METABOLISM; DNA REPAIR; DNA REPLICATION; DNA SUPERCOILING; DNA TRANSCRIPTION; DNA TRANSLOCATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBUNIT; EUKARYOTE; GENE TARGETING; GENE TRANSLOCATION; GENETIC REGULATION; GENOME; HISTONE MODIFICATION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOSOME; PHOTOAFFINITY LABELING; PHYSICAL MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; CARBOXY TERMINAL SEQUENCE; DNA HELIX; DNA SEQUENCE; DNA TRANSFER; GENE EXPRESSION REGULATION; HUMAN; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN PROCESSING; CHEMISTRY; METABOLISM;

EUKARYOTA;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; CHROMATIN ASSEMBLY AND DISASSEMBLY; NUCLEOSOMES; TRANSCRIPTION FACTORS;

EID: 84873689140     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-5037-5_13     Document Type: Article

References (131)

1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997;389:251-60.
2. Arents G, Moudrianakis EN. The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc Natl Acad Sci U S A. 1995;92:11170-4.
3. Andrews AJ, Luger K. Nucleosome structure(s) and stability: variations on a theme. Annu Rev Biophys. 2011;40:99-117.
4. Tan S, Davey CA. Nucleosome structural studies. Curr Opin Struct Biol. 2011;21:128-36.
5. Lowary PT, Widom J. New DNA sequence rules for high af fi nity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol. 1998;276:19-42.
6. Wu B, Mohideen K, Vasudevan D, Davey CA. Structural insight into the sequence dependence of nucleosome positioning. Structure. 2010;18:528-36.
7. Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, Wang MD. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat Struct Mol Biol. 2009;16:124-9.
8. Lavelle C, Prunell A. Chromatin polymorphism and the nucleosome superfamily: a genealogy. Cell Cycle. 2007;6:2113-9.
9. Zlatanova J, Bishop TC, Victor JM, Jackson V, van Holde K. The nucleosome family: dynamic and growing. Structure. 2009;17:160-71.
10. Bohm V, Hieb AR, Andrews AJ, Gansen A, Rocker A, Toth K, et al. Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res. 2011;39:3093-102.
11. Ulyanova NP, Schnitzler GR. Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates. Mol Cell Biol. 2005;25:11156-70.
12. Ulyanova NP, Schnitzler GR. Inverted factor access and slow reversion characterize SWI/ SNF-altered nucleosome dimers. J Biol Chem. 2007;282:1018-28.
13. Bancaud A, Wagner G, Conde ESN, Lavelle C, Wong H, Mozziconacci J, et al. Nucleosome chiral transition under positive torsional stress in single chromatin fi bers. Mol Cell. 2007;27:135-47.
14. Dalal Y, Furuyama T, Vermaak D, Henikoff S. Structure, dynamics, and evolution of centromeric nucleosomes. Proc Natl Acad Sci U S A. 2007;104:15974-81.
15. Woodcock CL, Ghosh RP. Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol. 2010;2:a000596.
16. Luger K, Hansen JC. Nucleosome and chromatin fi ber dynamics. Curr Opin Struct Biol. 2005;15:188-96.
17. Li G, Reinberg D. Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev. 2011;21:175-86.
18. Tremethick DJ. Higher-order structures of chromatin: the elusive 30 nm fi ber. Cell. 2007;128:651-4.
19. Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K. Structure and dynamic properties of nucleosome core particles. FEBS Lett. 2005;579:895-8.
20. Dorigo B, Schalch T, Kulangara A, Duda S, Schroeder RR, Richmond TJ. Nucleosome arrays reveal the two-start organization of the chromatin fi ber. Science. 2004;306:1571-3.
21. Belmont AS. Mitotic chromosome scaffold structure: new approaches to an old controversy. Proc Natl Acad Sci U S A. 2002;99:15855-7.
22. Muller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, McNally JG. Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol Cell Biol. 2004;24:9359-70.
23. Smith CL, Peterson CL. ATP-dependent chromatin remodeling. Curr Top Dev Biol. 2005;65:115-48.
24. Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem. 2009;78:273-304.
25. Fairman-Williams ME, Guenther UP, Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol. 2010;20:313-24.
26. Hopfner KP, Gerhold CB, Lakomek K, Wollmann P. Swi2/Snf2 remodelers: hybrid views on hybrid molecular machines. Curr Opin Struct Biol. 2012;22:225-33.
27. Hota SK, Bartholomew B. Diversity of operation in ATP-dependent chromatin remodelers. Biochim Biophys Acta. 2011;1809:476-87.
28. Kasten MM, Clapier CR, Cairns BR. SnapShot: chromatin remodeling: SWI/SNF. Cell. 2009;144(310):e311.
29. Liu N, Balliano A, Hayes JJ. Mechanism(s) of SWI/SNF-induced nucleosome mobilization. Chembiochem. 2011;12:196-204.
30. Hargreaves DC, Crabtree GR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 2011;21:396-420.
31. Erdel F, Rippe K. Chromatin remodelling in mammalian cells by ISWI-type complexes- where, when and why? FEBS J. 2011;278:3608-18.
32. Bao Y, Shen X. INO80 subfamily of chromatin remodeling complexes. Mutat Res. 2007;618:18-29.
33. Guillemette BT, Bataille AR, Gévry N, Adam M, Blanchette M, Robert FO, et al. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol. 2005;3:e384.
34. Durr H, Flaus A, Owen-Hughes T, Hopfner KP. Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res. 2006;34:4160-7.
35. Durr H, Korner C, Muller M, Hickmann V, Hopfner KP. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell. 2005;121:363-73.
36. Singleton MR, Dillingham MS, Wigley DB. Structure and mechanism of helicases and nucleic acid translocases. Annu Rev Biochem. 2007;76:23-50.
37. Quinn J, Fyrberg AM, Ganster RW, Schmidt MC, Peterson CL. DNA-binding properties of the yeast SWI/SNF complex. Nature. 1996;379:844-7.
38. Strohner R, Wachsmuth M, Dachauer K, Mazurkiewicz J, Hochstatter J, Rippe K, et al. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol. 2005;12:683-90.
39. Zofall M, Persinger J, Kassabov SR, Bartholomew B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat Struct Mol Biol. 2006;13:339-46.
40. Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol. 2005;12:747-55.
41. Schwanbeck R, Xiao H, Wu C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J Biol Chem. 2004;279:39933-41.
42. Kagalwala MN, Glaus BJ, Dang W, Zofall M, Bartholomew B. Topography of the ISW2- nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 2004;23:2092-104.
43. Chaban Y, Ezeokonkwo C, Chung WH, Zhang F, Kornberg RD, Maier-Davis B, et al. Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol. 2008;15:1272-7.
44. Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, et al. Conformational fl exibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A. 2007;104:4913-8.
45. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, et al. Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol. 2008;28:6010-21.
46. Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, Bartholomew B. Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res. 2012;40:4412-21.
47. Dang W, Kagalwala MN, Bartholomew B. The Dpb4 subunit of ISW2 is anchored to extranucleosomal DNA. J Biol Chem. 2007;282:19418-25.
48. Gangaraju VK, Bartholomew B. Dependency of ISW1a chromatin remodeling on extranucleosomal DNA. Mol Cell Biol. 2007;27:3217-25.
49. Dang W, Bartholomew B. Domain architecture of the catalytic subunit in the ISW2- nucleosome complex. Mol Cell Biol. 2007;27:8306-17.
50. Yang JG, Madrid TS, Sevastopoulos E, Narlikar GJ. The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat Struct Mol Biol. 2006;13:1078-83.
51. Gangaraju VK, Prasad P, Srour A, Kagalwala MN, Bartholomew B. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol Cell. 2009;35:58-69.
52. Zofall M, Persinger J, Bartholomew B. Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2. Mol Cell Biol. 2004;24:10047-57.
53. Gangaraju VK, Bartholomew B. Mechanisms of ATP dependent chromatin remodeling. Mutat Res. 2007;618:3-17.
54. Jaskelioff M, Van Komen S, Krebs JE, Sung P, Peterson CL. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J Biol Chem. 2003;278:9212-8.
55. Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 2002;16:2120-34.
56. Whitehouse I, Stockdale C, Flaus A, Szczelkun MD, Owen-Hughes T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol Cell Biol. 2003;23:1935-45.
57. Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DM, et al. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell. 2000;103:1133-42.
58. Gavin I, Horn PJ, Peterson CL. SWI/SNF chromatin remodeling requires changes in DNA topology. Mol Cell. 2001;7:97-104.
59. Solinger JA, Kiianitsa K, Heyer WD. Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA fi laments. Mol Cell. 2002;10:1175-88.
60. Amitani I, Baskin RJ, Kowalczykowski SC. Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules. Mol Cell. 2006;23:143-8.
61. Prasad TK, Robertson RB, Visnapuu ML, Chi P, Sung P, Greene EC. A DNA-translocating Snf2 molecular motor: Saccharomyces cerevisiae Rdh54 displays processive translocation and extrudes DNA loops. J Mol Biol. 2007;369:940-53.
62. Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC, Dunlap D, et al. Direct observation of DNA distortion by the RSC complex. Mol Cell. 2006;21:417-25.
63. Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J. 2011;30:2364-72.
64. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006;24:559-68.
65. Imbalzano AN, Kwon H, Green MR, Kingston RE. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature. 1994;370:481-5.
66. Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature. 1994;370:477-81.
67. Hota SK, Bartholomew B. Approaches for studying nucleosome movement by ATPdependent chromatin remodeling complexes. Methods Mol Biol. 2012;809:367-80.
68. Hota SK, Dechassa ML, Prasad P, Bartholomew B. Mapping protein-DNA and protein-protein interactions of ATP-dependent chromatin remodelers. Methods Mol Biol. 2012;809:381-409.
69. Sengupta SM, VanKanegan M, Persinger J, Logie C, Cairns BR, Peterson CL, et al. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J Biol Chem. 2001;276:12636-44.
70. Kassabov SR, Zhang B, Persinger J , Bartholomew B. Sucleosome . Mol Cell. 2003;11: 391-403.
71. Alexeev A, Mazin A, Kowalczykowski SC. Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein fi lament. Nat Struct Biol. 2003;10:182-6.
72. Shundrovsky A, Smith CL, Lis JT, Peterson CL, Wang MD. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol. 2006;13:549-54.
73. Bouazoune K, Miranda TB, Jones PA, Kingston RE. Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res. 2009;37:5279-94.
74. Kassabov SR, Henry NM, Zofall M, Tsukiyama T, Bartholomew B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol Cell Biol.2002;22:7524-34.
75. Hamiche A, Sandaltzopoulos R, Gdula DA, Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell. 1999;97:833-42.
76. Langst G, Bonte EJ, Corona DF, Becker PB. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell. 1999;97:843-52.
77. van Vugt JJ, de Jager M, Murawska M, Brehm A, van Noort J, Logie C. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS One. 2009;4:e6345.
78. Stockdale C, Flaus A, Ferreira H, Owen-Hughes T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem. 2006;281:16279-88.
79. Udugama M, Sabri A, Bartholomew B. The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor. Mol Cell Biol. 2011;31:662-73.
80. Fyodorov DV, Blower MD, Karpen GH, Kadonaga JT. Acf1 confers unique activities to ACF/ CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 2004;18:170-83.
81. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT. ACF, an ISWI-containing and ATPutilizing chromatin assembly and remodeling factor. Cell. 1997;90:145-55.
82. Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. Dynamics of nucleosome remodelling by individual ACF complexes. Nature. 2009;462:1022-7.
83. Narlikar GJ. A proposal for kinetic proof reading by ISWI family chromatin remodeling motors. Curr Opin Chem Biol. 2010;14:660-5.
84. Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, et al. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature. 2009;462:1016-21.
85. Ong MS, Richmond TJ, Davey CA. DNA stretching and extreme kinking in the nucleosome core. J Mol Biol. 2007;368:1067-74.
86. Aoyagi S, Narlikar G, Zheng C, Sif S, Kingston RE, Hayes JJ. Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions. Mol Cell Biol. 2002;22:3653-62.
87. Cairns BR. Chromatin remodeling: insights and intrigue from single-molecule studies. Nat Struct Mol Biol. 2007;14:989-96.
88. Liu N, Peterson CL, Hayes JJ. SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol. 2011;31:4165-75.
89. Bowman GD. Mechanisms of ATP-dependent nucleosome sliding. Curr Opin Struct Biol. 2010;20:73-81.
90. Leschziner AE. Electron microscopy studies of nucleosome remodelers. Curr Opin Struct Biol. 2011;21:709-18
91. Racki LR, Narlikar GJ. ATP-dependent chromatin remodeling enzymes: two heads are not better, just different. Curr Opin Genet Dev. 2008;18:137-44.
92. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, et al. Structure and mechanism of the chromatin remodelling factor ISW1a. Nature. 2011;472:448-53.
93. Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, Reinberg D. FACT facilitates transcription-dependent nucleosome alteration. Science. 2003;301:1090-3.
94. Bruno M, Flaus A, Stockdale C, Rencurel C, Ferreira H, Owen-Hughes T. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol Cell. 2003;12:1599-606.
95. Vicent GP, Nacht AS, Smith CL, Peterson CL, Dimitrov S, Beato M. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol Cell. 2004;16:439-52.
96. Cote J, Quinn J, Workman JL, Peterson CL. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994;265:53-60.
97. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2004;303:343-8.
98. Suto RK, Clarkson MJ, Tremethick DJ, Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol. 2000;7:1121-4.
99. Schnitzler G, Sif S, Kingston RE. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell. 1998;94:17-27.
100. Schnitzler GR, Cheung CL, Hafner JH, Saurin AJ, Kingston RE, Lieber CM. Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol Cell Biol. 2001;21:8504-11.
101. Lorch Y, Cairns BR, Zhang M, Kornberg RD. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell. 1998;94:29-34.
102. Phelan ML, Schnitzler GR, Kingston RE. Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases. Mol Cell Biol. 2000;20:6380-9.
103. Bash R, Wang H, Anderson C, Yodh J, Hager G, Lindsay SM, et al. AFM imaging of protein movements: histone H2A-H2B release during nucleosome remodeling. FEBS Lett. 2006;580:4757-61.
104. Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N, Kladde MP, et al. SWI/ SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol Cell. 2010;38:590-602.
105. Park YJ, Luger K. Histone chaperones in nucleosome eviction and histone exchange. Curr Opin Struct Biol. 2008;18:282-9.
106. Engeholm M, de Jager M, Flaus A, Brenk R, van Noort J, Owen-Hughes T. Nucleosomes can invade DNA territories occupied by their neighbors. Nat Struct Mol Biol. 2009;16:151-8.
107. De Cian A, Praly E, Ding F, Singh V, Lavelle C, Le Cam E, et al. ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA. PLoS One. 2012;7:e31845.
108. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128:693-705.
109. Shogren-Knaak M, Ishii H, Sun J-M, Pazin MJ, Davie JR, Peterson CL. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 2006;311:844-7.
110. Gardner KE, Allis C, Strahl BD. Operating on chromatin, a colorful language where context matters. J Mol Biol. 2011;409:36-46.
111. Suganuma T, Workman JL. Signals and combinatorial functions of histone modifications. Annu Rev Biochem. 2011;80:473-99.
112. Ferreira H, Flaus A, Owen-Hughes T. Histone modifications in fl uence the action of Snf2 family remodelling enzymes by different mechanisms. J Mol Biol. 2007;374:563-79.
113. Clapier CR, Langst G, Corona DF, Becker PB, Nightingale KP. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol Cell Biol. 2001;21:875-83.
114. Clapier CR, Nightingale KP, Becker PB. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 2002;30:649-55.
115. Erdel F, Krug J, Langst G, Rippe K. Targeting chromatin remodelers: signals and search mechanisms. Biochim Biophys Acta. 2011;1809:497-508.
116. Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, Langst G. DNA sequence- and conformation- directed positioning of nucleosomes by chromatin-remodeling complexes. Proc Natl Acad Sci U S A. 2007;104:15635-40.
117. Goldman JA, Garlick JD, Kingston RE. Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z. J Biol Chem. 2010;285:4645-51.
118. Hauk G, McKnight JN, Nodelman IM, Bowman GD. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell. 2010;39:711-23.
119. Hassan AH, Awad S, Al-Natour Z, Othman S, Mustafa F, Rizvi TA. Selective recognition of acetylated histones by bromodomains in transcriptional co-activators. Biochem J. 2007;402:125-33.
120. Glatt S, Al fi eri C, Muller CW. Recognizing and remodeling the nucleosome. Curr Opin Struct Biol. 2011;21:335-41.
121. Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, et al. A PHD fi nger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature. 2006;442:86-90.
122. Das C, Tyler JK, Churchill ME. The histone shuf fl e: histone chaperones in an energetic dance. Trends Biochem Sci. 2010;35:476-89.
123. Ransom M, Dennehey BK, Tyler JK. Chaperoning histones during DNA replication and repair. Cell. 2010;140:183-95.
124. Alabert C, Groth A. Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol. 2012;13:153-67.
125. Morrison AJ, Shen X. Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. Nat Rev Mol Cell Biol. 2009;10:373-84.
126. Jayani RS, Ramanujam PL, Galande S. Studying histone modifications and their genomic functions by employing chromatin immunoprecipitation and immunoblotting. Methods Cell Biol. 2010;98:35-56.
127. Truax AD, Greer SF. ChIP and Re-ChIP assays: investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind. Methods Mol Biol. 2012;809:175-88.
128. Erdel F, Rippe K. Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism. Nucleus. 2012;2:105-12.
129. Erdel F, Schubert T, Marth C, Langst G, Rippe K. Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc Natl Acad Sci U S A. 2010;107:19873-8.
130. Blossey R, Schiessel H. Kinetic proofreading of gene activation by chromatin remodeling. HFSP J. 2008;2:167-70.
131. Leschziner AE. Electron microscopy studies of nucleosome remodelers. Curr Opin Struct Biol. 2011;21:709-18.