Nucleosome sliding by Chd1 does not require rigid coupling between DNA-binding and ATPase domains

EMBO Reports

Volumn 14, Issue 12, 2013, Pages 1098-1103

  Nodelman, Ilana M ^a   Bowman, Gregory D ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Chd1; Chromatin remodeller; Nucleosome sliding

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA; CHD1 PROTEIN, S CEREVISIAE; DNA BINDING PROTEIN; NUCLEOSOME; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHROMATIN; DNA BINDING; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; ANIMAL; CHEMISTRY; CHROMATIN ASSEMBLY AND DISASSEMBLY; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; METABOLISM; SACCHAROMYCES CEREVISIAE; XENOPUS;

ADENOSINE TRIPHOSPHATASES; ANIMALS; CATALYTIC DOMAIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA; DNA-BINDING PROTEINS; NUCLEOSOMES; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; XENOPUS;

EID: 84889084190     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/embor.2013.158     Document Type: Article

References (25)

1. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128: 707-719
2. Cairns BR (2009) The logic of chromatin architecture and remodelling at promoters. Nature 461: 193-198
3. Ryan DP, Owen-Hughes T (2011) Snf2-family proteins: Chromatin remodellers for any occasion. Curr Opin Chem Biol 15: 649-656
4. Hota SK, Bartholomew B (2011) Diversity of operation in ATP-dependent chromatin remodelers. Biochim Biophys Acta 1809: 476-487
5. Gru?ne T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Mu? ller CW (2003) Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cell 12: 449-460
6. 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
7. 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
8. Patel A, McKnight JN, Genzor P, Bowman GD (2011) Identification of residues in chromo-helicase-DNA-binding protein 1 (Chd1) required for coupling ATP hydrolysis to nucleosome sliding. J Biol Chem 286: 43984-43993
9. Saha A, Wittmeyer J, Cairns BR (2006) Chromatin remodelling: The industrial revolution of DNA around histones. Nat Rev Mol Cell Biol 7: 437-447
10. Cairns BR (2007) Chromatin remodeling: Insights and intrigue from single-molecule studies. Nat Struct Mol Biol 14: 989-996
11. 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
12. Mu? ller-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
13. Clapier CR, Cairns BR (2012) Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492: 280-284
14. Patel A, Chakravarthy S, Morrone S, Nodelman IM, McKnight JN, Bowman GD (2013) Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler. Nucleic Acids Res 41: 1637-1648
15. 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
16. Forne I, Ludwigsen J, Imhof A, Becker PB, Mu? ller-Planitz F (2012) Probing the conformation of the ISWI ATPase domain with genetically encoded photoreactive cross-linkers and mass spectrometry. Mol Cell Proteomics 11: M111.012088.1-11
17. Stockdale C, Flaus A, Ferreira H, Owen-Hughes T (2006) Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem 281: 16279-16288
18. Yang JG, Madrid TS, Sevastopoulos E, Narlikar GJ (2006) The chromatinremodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat Struct Mol Biol 13: 1078-1083
19. Bertagna A, Toptygin D, Brand L, Barrick D (2008) The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: A case of biologically tuned disorder. Biochem Soc Trans 36: 157-166
20. Zweifel ME, Leahy DJ, Hughson FM, Barrick D (2003) Structure and stability of the ankyrin domain of the Drosophila Notch receptor. Protein Sci 12: 2622-2632
21. Ludwigsen J, Klinker H, Mueller-Planitz F (2013) No need for a power stroke in ISWI-mediated nucleosome sliding. EMBO Rep 14: 1092-1097
22. 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
23. Luger K, Rechsteiner TJ, Richmond TJ (1999) Preparation of nucleosome core particle from recombinant histones. Methods Enzymol 304: 3-19
24. Lowary PT, Widom J (1998) New DNA sequence rules for high-affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19-42
25. Kiianitsa K, Solinger JA, Heyer WD (2003) NADH-coupled microplate photometric assay for kinetic studies of ATP-hydrolyzing enzymes with low and high-specific activities. Anal Biochem 321: 266-271