No need for a power stroke in ISWI-mediated nucleosome sliding

EMBO Reports

Volumn 14, Issue 12, 2013, Pages 1092-1097

  Ludwigsen, Johanna ^a   Klinker, Henrike ^a   Mueller Planitz, Felix ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

Chromatin remodelling; ISWI; Nucleosome sliding

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA; ENZYME; ISWI ENZYME; UNCLASSIFIED DRUG; ISWI PROTEIN; NUCLEOSOME; TRANSCRIPTION FACTOR;

ARTICLE; ASSAY; BIOCHEMICAL COMPOSITION; CATALYSIS; CONFORMATIONAL TRANSITION; DNA FLANKING REGION; ENZYME ASSAY; ENZYME CONFORMATION; EUKARYOTE; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; NONHUMAN; NUCLEOSOME; POWER STROKE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; ANIMAL; CHEMISTRY; CHROMATIN ASSEMBLY AND DISASSEMBLY; DROSOPHILA MELANOGASTER; ENZYMOLOGY; GENETICS; METABOLISM; PROTEIN TERTIARY STRUCTURE;

EUKARYOTA;

ADENOSINE TRIPHOSPHATASES; ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DROSOPHILA MELANOGASTER; NUCLEOSOMES; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS;

EID: 84889078670     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/embor.2013.160     Document Type: Article

References (31)

1. Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78: 273-304
2. Flaus A, Martin DM, Barton GJ, Owen-Hughes T (2006) Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 34: 2887-2905
3. Saha A, Wittmeyer J, Cairns BR (2002) Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev 16: 2120-2134
4. Whitehouse I, Stockdale C, Flaus A, Szczelkun MD, Owen-Hughes T (2003) Evidence for DNA translocation by the ISWI chromatinremodeling enzyme. Mol Cell Biol 23: 1935-1945
5. Zofall M, Persinger J, Kassabov SR, Bartholomew B (2006) Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat Struct Mol Biol 13: 339-346
6. Saha A, Wittmeyer J, Cairns BR (2005) Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 12: 747-755
7. Schwanbeck R, Xiao H, Wu C (2004) Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J Biol Chem 279: 39933-39941
8. Dang W, Kagalwala MN, Bartholomew B (2006) Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Mol Cell Biol 26: 7388-7396
9. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, Bartholomew B (2008) Architecture of the SWI/SNFnucleosome complex. Mol Cell Biol 28: 6010-6021
10. Hota SK, Bhardwaj SK, Deindl S, Lin YC, Zhuang X, Bartholomew B (2013) Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat Struct Mol Biol 20: 222-229
11. Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X (2013) ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 152: 442-452
12. Langst G, Becker PB (2001) ISWI induces nucleosome sliding on nicked DNA. Mol Cell 8: 1085-1092
13. Strohner R, Wachsmuth M, Dachauer K, Mazurkiewicz J, Hochstatter J, Rippe K, Langst G (2005) A 'loop recapture' mechanism for ACFdependent nucleosome remodeling. Nat Struct Mol Biol 12: 683-690
14. Dang W, Bartholomew B (2007) Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol Cell Biol 27: 8306-8317
15. Mueller-Planitz F, Klinker H, Ludwigsen J, Becker PB (2013) The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat Struct Mol Biol 20: 82-89
16. Clapier CR, Cairns BR (2012) Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492: 280-284
17. Ryan DP, Sundaramoorthy R, Martin D, Singh V, Owen-Hughes T (2011) The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J 30: 2596-2609
18. McKnight JN, Jenkins KR, Nodelman IM, Escobar T, Bowman GD (2011) Extranucleosomal DNA binding directs nucleosome sliding by Chd1. Mol Cell Biol 31: 4746-4759
19. Hauk G, McKnight JN, Nodelman IM, Bowman GD (2010) The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell 39: 711-723
20. Grune T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Muller CW (2003) Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cel 449-460
21. Yildiz A, Tomishige M, Gennerich A, Vale RD (2008) Intramolecular strain coordinates kinesin stepping behavior along microtubules. Cell 134: 1030-1041
22. Hackney DD, Stock MF, Moore J, Patterson RA (2003) Modulation of kinesin half-site ADP release and kinetic processivity by a spacer between the head groups. Biochemistry 42: 12011-12018
23. Evers TH, van Dongen EM, Faesen AC, Meijer EW, Merkx M (2006) Quantitative understanding of the energy transfer between fluorescent proteins connected via flexible peptide linkers. Biochemistry 45: 13183-13192
24. Sahoo H, Roccatano D, Zacharias M, Nau WM (2006) Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain. J Am Chem Soc 128: 8118-8119
25. Forne I, Ludwigsen J, Imhof A, Becker PB, Mueller-Planitz F (2012) Probing the conformation of the ISWI ATPase domain with genetically encoded photoreactive crosslinkers and mass spectrometry. Mol Cell Proteomics 11: M111 012088
26. Nodelman IM, Bowman GD (2013) Nucleosome sliding by Chd1 does not require rigid coupling between DNA-binding and ATPase domains. EMBO Rep 14: 1098-1103
27. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ (2011) Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472: 448-453
28. Gangaraju VK, Prasad P, Srour A, Kagalwala MN, Bartholomew B (2009) Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol Cell 35: 58-69
29. Lorch Y, Maier-Davis B, Kornberg RD (2010) Mechanism of chromatin remodeling. Proc Natl Acad Sci USA 107: 3458-3462
30. Klock HE, Lesley SA (2009) The polymerase incomplete primer extension (PIPE) method applied to high-throughput cloning and site-directed mutagenesis. Methods Mol Biol 498: 91-103
31. Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K (2004) Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol 375: 23-44