Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure

Nature

Volumn 544, Issue 7651, 2017, Pages 440-445

  Liu, Xiaoyu ^a,b   Li, Meijing ^a,b   Xia, Xian ^a   Li, Xueming ^a,b   Chen, Zhucheng ^a  

^a TSINGHUA UNIVERSITY   (China)

^b Tsinghua University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; FUNGAL PROTEIN; HELICASE; SNF2 PROTEIN; UNCLASSIFIED DRUG; ADENOSINE TRIPHOSPHATASE; HISTONE; NUCLEOSOME; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN; SNF2 PROTEIN, S CEREVISIAE; TRANSCRIPTION FACTOR;

CHEMICAL BINDING; CHROMOSOME; DNA; ELECTRON MICROSCOPY; ENZYME ACTIVITY; HYDROLYSIS; MOLECULAR ANALYSIS; PHOSPHATE; PROTEIN; SUBSTRATE; YEAST;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; HYDROLYSIS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SURFACE PROPERTY; AMINO ACID SEQUENCE; BINDING SITE; CHEMISTRY; ENZYMOLOGY; METABOLISM; MOLECULAR MODEL; ULTRASTRUCTURE;

SACCHAROMYCES CEREVISIAE;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; BINDING SITES; CHROMATIN ASSEMBLY AND DISASSEMBLY; CRYOELECTRON MICROSCOPY; DNA; HISTONES; MODELS, MOLECULAR; NUCLEOSOMES; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 85018736844     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature22036     Document Type: Article

References (44)

1. Clapier, C. R., & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304 (2009
2. Narlikar, G. J., Sundaramoorthy, R., & Owen-Hughes, T. Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154, 490-503 (2013
3. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251-260 (1997
4. Saha, A., Wittmeyer, J., & Cairns, B. R. Chromatin remodelling: the industrial revolution of DNA around histones. Nature Rev. Mol. Cell Biol. 7, 437-447 (2006
5. Becker, P. B., & Hörz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247-273 (2002
6. Mueller-Planitz, F., Klinker, H., & Becker, P. B. Nucleosome sliding mechanisms: new twists in a looped history. Nature Struct. Mol. Biol. 20, 1026-1032 (2013
7. Xia, X., Liu, X., Li, T., Fang, X., & Chen, Z. Structure of chromatin remodeler Swi2/Snf2 in the resting state. Nature Struct. Mol. Biol. 23, 722-729 (2016
8. Hauk, G., McKnight, J. N., Nodelman, I. M., & Bowman, G. D. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol. Cell 39, 711-723 (2010
9. Yan, L., Wang, L., Tian, Y., Xia, X., & Chen, Z. Structure and regulation of the chromatin remodeller ISWI. Nature 540, 466-469 (2016
10. Leschziner, A. E. Electron microscopy studies of nucleosome remodelers. Curr. Opin. Struct. Biol. 21, 709-718 (2011
11. Watanabe, S., et al. Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nature Commun. 6, 7108 (2015
12. Tosi, A., et al. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 154, 1207-1219 (2013
13. Nguyen, V. Q., et al. Molecular architecture of the ATP-dependent chromatinremodeling complex SWR1. Cell 154, 1220-1231 (2013
14. Yamada, K., et al. Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472, 448-453 (2011
15. Racki, L. R., et al. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462, 1016-1021 (2009
16. Leschziner, A. E., Lemon, B., Tjian, R., & Nogales, E. Structural studies of the human PBAF chromatin-remodeling complex. Structure 13, 267-275 (2005
17. Lowary, P. T., & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19-42 (1998
18. Zofall, M., Persinger, J., Kassabov, S. R., & Bartholomew, B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nature Struct. Mol. Biol. 13, 339-346 (2006
19. Dechassa, M. L., et al. Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res. 40, 4412-4421 (2012
20. Dechassa, M. L., et al. Architecture of the SWI/SNF-nucleosome complex. Mol. Cell. Biol. 28, 6010-6021 (2008
21. Makde, R. D., England, J. R., Yennawar, H. P., & Tan, S. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562-566 (2010
22. Clapier, C. R., et al. Regulation of DNA translocation efficiency within the chromatin remodeler RSC/Sth1 potentiates nucleosome sliding and ejection. Mol. Cell 62, 453-461 (2016
23. Szerlong, H., et al. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nature Struct. Mol. Biol. 15, 469-476 (2008
24. Fan, H. Y., Trotter, K. W., Archer, T. K., & Kingston, R. E. Swapping function of two chromatin remodeling complexes. Mol. Cell 17, 805-815 (2005
25. Clapier, C. R., & Cairns, B. R. Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492, 280-284 (2012
26. Dürr, H., Körner, C., Müller, M., Hickmann, V., & Hopfner, K. P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121, 363-373 (2005
27. Smith, C. L., & Peterson, C. L. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol. Cell. Biol. 25, 5880-5892 (2005
28. Saha, A., Wittmeyer, J., & Cairns, B. R. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nature Struct. Mol. Biol. 12, 747-755 (2005
29. Gu, M., & Rice, C. M. Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc. Natl Acad. Sci. USA 107, 521-528 (2010
30. Harada, B. T., et al. Stepwise nucleosome translocation by RSC remodeling complexes. eLife 5, 5 (2016
31. Tan, S., & Davey, C. A. Nucleosome structural studies. Curr. Opin. Struct. Biol. 21, 128-136 (2011
32. Mueller-Planitz, F., Klinker, H., Ludwigsen, J., & Becker, P. B. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nature Struct. Mol. Biol. 20, 82-89 (2013
33. Ong, M. S., Richmond, T. J., & Davey, C. A. DNA stretching and extreme kinking in the nucleosome core. J. Mol. Biol. 368, 1067-1074 (2007
34. Stark, H. GraFix: Stabilization of Fragile Macromolecular Complexes for Single Particle Cryo-EM. Methods Enzymol. 481, 109-126 (2010
35. Li, X., Zheng, S., Agard, D. A., & Cheng, Y. Asynchronous data acquisition and on-The-fly analysis of dose fractionated cryoEM images by UCSFImage. J. Struct. Biol. 192, 174-178 (2015
36. Mindell, J. A., & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347 (2003
37. Ludtke, S. J. 3-D structures of macromolecules using single-particle analysis in EMAN. Methods Mol. Biol. 673, 157-173 (2010
38. Bharat, T. A., Russo, C. J., Löwe, J., Passmore, L. A., & Scheres, S. H. Advances in single-particle electron cryomicroscopy structure determination applied to sub-Tomogram averaging. Structure 23, 1743-1753 (2015
39. Frank, J., et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190-199 (1996
40. Li, X., et al. Electron Counting and Beam-induced Motion Correction Enable Near-Atomic-resolution Single-particle Cryo-EM. Nature Methods 10, 584-590 (2013
41. Scheres, S. H., & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nature Methods 9, 853-854 (2012
42. Bai, X. C., Rajendra, E., Yang, G., Shi, Y., & Scheres, S. H. Sampling the conformational space of the catalytic subunit of human ? -secretase. eLife 4, 4 (2015
43. Pettersen, E. F., et al. UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004
44. Afonine, P. V., et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352-367 (2012