1932

Abstract

A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biochem-051810-093157
2014-06-02
2024-06-21
Loading full text...

Full text loading...

/deliver/fulltext/biochem/83/1/annurev-biochem-051810-093157.html?itemId=/content/journals/10.1146/annurev-biochem-051810-093157&mimeType=html&fmt=ahah

Literature Cited

  1. Flaus A, Martin DMA, Barton GJ, Owen-Hughes T. 1.  2006. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res. 34:2887–905 [Google Scholar]
  2. Ho L, Crabtree GR. 2.  2010. Chromatin remodelling during development. Nature 463:474–84 [Google Scholar]
  3. Ronan JL, Wu W, Crabtree GR. 3.  2013. From neural development to cognition: unexpected roles for chromatin. Nat. Rev. Genet. 14:347–59 [Google Scholar]
  4. Sims JK, Wade PA. 4.  2011. SnapShot: Chromatin remodeling: CHD. Cell 144:626e1 [Google Scholar]
  5. Yoo AS, Crabtree GR. 5.  2009. ATP-dependent chromatin remodeling in neural development. Curr. Opin. Neurobiol. 19:120–26 [Google Scholar]
  6. Lessard J, Wu JI, Ranish JA, Wan M, Windlow MM. 6.  et al. 2007. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55:201–15 [Google Scholar]
  7. Yoo AS, Staahl BT, Chen L, Crabtree GR. 7.  2009. MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature 460:642–46 [Google Scholar]
  8. Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N. 8.  et al. 2010. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol. Cell 38:590–602 [Google Scholar]
  9. Boeger H, Griesenbeck J, Kornberg RD. 9.  2008. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133:716–26 [Google Scholar]
  10. Boeger H, Griesenbech J, Strattan JS, Kornberg RD. 10.  2004. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell 14:667–73 [Google Scholar]
  11. Luk E, Ranjan A, Fitzgerald PC, Mizuguchi G, Huang Y. 11.  et al. 2010. Stepwise histone replacement by SWR1 requires dual activation with histone H2A. Z and canonical nucleosome Cell 143:725–36 [Google Scholar]
  12. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. 12.  2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343–48 [Google Scholar]
  13. Papamichos-Chronakis M, Watanabe S, Rando OJ, Peterson CL. 13.  2011. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell 144:200–13 [Google Scholar]
  14. Loyola A, LeRoy G, Wang YH, Reinberg D. 14.  2001. Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev. 15:2837–51 [Google Scholar]
  15. Walfridsson J, Bjerling P, Thalen M, Yoo E-J, Park SD, Ekwall K. 15.  2005. The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres. Nucleic Acids Res. 33:2868–79 [Google Scholar]
  16. Robinson KM, Schultz MC. 16.  2003. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol. Cell. Biol. 23:7937–46 [Google Scholar]
  17. Konev AY, Tribus M, Park SY, Lim CY, Emelyanov AV. 17.  et al. 2007. CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo. Science 317:1087–90 [Google Scholar]
  18. Lusser A, Urwin DL, Kadonaga JT. 18.  2005. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12:160–66 [Google Scholar]
  19. Drané P, Ouararhni K, Depaux A, Shuaib M, Hamiche A. 19.  2010. The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev. 24:1253–65 [Google Scholar]
  20. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsässer SJ. 20.  et al. 2010. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140:678–91 [Google Scholar]
  21. Lewis PW, Elsässer SJ, Noh KM, Stadler SC, Allis CD. 21.  2010. Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres. Proc. Natl. Acad. Sci. USA 107:14075–80 [Google Scholar]
  22. Baumann C, Viveiros MM, De La Fuente R. 22.  2010. Loss of maternal ATRX results in centromere instability and aneuploidy in the mammalian oocyte and pre-implantation embryo. PLoS Genet. 6:e1001137 [Google Scholar]
  23. Heaphy CM, de Wilde RF, Jiao Y, Edil BH, Shi C. 23.  et al. 2011. Altered telomeres in tumors with ATRX and DAXX mutations. Science 333:425 [Google Scholar]
  24. Bower K, Napier CE, Cole SL, Dagg RA, Lau LMS. 24.  et al. 2012. Loss of wild-type ATRX expression in somatic cell hybrids segregates with activation of alternative lengthening of telomeres. PLoS ONE 7:e50062 [Google Scholar]
  25. Perpelescu M, Nozaki N, Obuse C, Yang H, Yoda K. 25.  2009. Active establishment of centromeric CENP-A chromatin by RSF complex. J. Cell Biol. 185:397–407 [Google Scholar]
  26. Dang W, Bartholomew B. 26.  2007. Domain architecture of the catalytic subunit in the ISW2–nucleosome complex. Mol. Cell. Biol. 27:8306–17 [Google Scholar]
  27. Hota SK, Bhardwaj SK, Deindl S, Lin YC, Zhuang X, Bartholomew B. 27.  2013. Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat. Struct. Mol. Biol. 20:222–29 [Google Scholar]
  28. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL. 28.  et al. 2008. Architecture of the SWI/SNF–nucleosome complex. Mol. Cell. Biol. 28:6010–21 [Google Scholar]
  29. Hauk G, McKnight JN, Nodelman IN, Bowman GD. 29.  2010. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol. Cell 39:711–23 [Google Scholar]
  30. Thoma NH, Czyzewski BK, Alexeev AA, Mazin AV, Kowalczykowski SC, Pavletich NP. 30.  2005. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12:350–56 [Google Scholar]
  31. Durr H, Körner C, Müller M, Hickmann V, Hopfner KP. 31.  2005. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121:363–73 [Google Scholar]
  32. Wollmann P, Cui S, Viswanathan R, Berninghausen O, Wells MN. 32.  et al. 2011. Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP. Nature 475:403–7 [Google Scholar]
  33. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM. 33.  1988. A conserved NTP motif in putative helicases. Nature 333:22 [Google Scholar]
  34. Gorbalenya AE, Koonin EV. 34.  1993. Helicases: amino acid sequence comparisons and structure–function relationship. Curr. Opin. Struct. Biol. 3:419–29 [Google Scholar]
  35. Eisen JA, Sweder KS, Hanawalt PC. 35.  1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23:2715–23 [Google Scholar]
  36. Szerlong H, Hinata K, Viswanathan R, Erdjument-Bromage H, Tempst P, Cairns BR. 36.  2008. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat. Struct. Mol. Biol. 15:469–76 [Google Scholar]
  37. Dumont S, Cheng W, Serebrov V, Beran RJ, Tinoco I Jr. 37.  et al. 2006. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439:105–8 [Google Scholar]
  38. Myong S, Bruno MM, Pyle AM, Ha T. 38.  2007. Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science 317:513–16 [Google Scholar]
  39. Cheng W, Arunajadai SG, Moffitt JR, Tinoco I Jr, Bustamante C. 39.  2011. Single–base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase. Science 333:1746–49 [Google Scholar]
  40. Dillingham MS, Wigley DB, Webb MR. 40.  2000. Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry 39:205–12 [Google Scholar]
  41. Lee JY, Yang W. 41.  2006. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell 127:1349–60 [Google Scholar]
  42. Park J, Myong S, Niedziela-Majka A, Lee KS, Yu J. 42.  et al. 2010. PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. Cell 142:544–55 [Google Scholar]
  43. Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P. 43.  et al. 2013. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 152:442–52 [Google Scholar]
  44. Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G. 44.  1997. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90:635–47 [Google Scholar]
  45. Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB. 45.  1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97:75–84 [Google Scholar]
  46. Singleton MR, Dillingham MS, Wigley DB. 46.  2007. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76:23–50 [Google Scholar]
  47. Dechassa ML, Hota SK, Sen P, Chatterjee N, Prasad P, Bartholomew B. 47.  2012. Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res. 40:4412–21 [Google Scholar]
  48. Elsässer SJ, Huang H, Lewis PW, Chin JW, Allis CD, Patel DJ. 48.  2012. DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition. Nature 491:560–65 [Google Scholar]
  49. Saha A, Wittmeyer J, Cairns BR. 49.  2005. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12:747–55 [Google Scholar]
  50. Schwanbeck R, Xiao H, Wu C. 50.  2004. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279:39933–41 [Google Scholar]
  51. Zofall M, Persinger J, Kassabov SR, Bartholomew B. 51.  2006. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 13:339–46 [Google Scholar]
  52. Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY. 52.  et al. 2006. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442:86–90 [Google Scholar]
  53. Li H, Ilin S, Wang W, Duncan EM, Wysocka J. 53.  et al. 2006. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442:91–95 [Google Scholar]
  54. Thompson M.54.  2009. Polybromo-1: the chromatin targeting subunit of the PBAF complex. Biochimie 91:309–19 [Google Scholar]
  55. Chandrasekaran R, Thompson M. 55.  2007. Polybromo-L-bromodomains bind histone H3 at specific acetyl-lysine positions. Biochem. Biophys. Res. Commun. 355:661–66 [Google Scholar]
  56. Goodwin GH, Nicolas RH. 56.  2001. The BAH domain, polybromo and the RSC chromatin remodelling complex. Gene 268:1–7 [Google Scholar]
  57. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 57.  2007. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14:1025–40 [Google Scholar]
  58. Patel DJ, Wang Z. 58.  2013. Readout of epigenetic modifications. Annu. Rev. Biochem. 82:81–118 [Google Scholar]
  59. Eustermann S, Yang JC, Amos R, Chapman LM, Jelinska C. 59.  et al. 2011. Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nat. Struct. Mol. Biol. 18:777–82 [Google Scholar]
  60. Argentaro A, Chang J-C, Chapman LM, Kowalczyk MS, Gibbons RJ. 60.  et al. 2007. Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX. Proc. Natl. Acad. Sci. USA 104:11939–44 [Google Scholar]
  61. Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y. 61.  et al. 2012. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat. Struct. Mol. Biol. 19:884–92 [Google Scholar]
  62. Maltby VE, Martin BJ, Schultze JM, Johnson I, Hentrich T. 62.  et al. 2012. Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin. Mol. Cell. Biol. 32:3479–85 [Google Scholar]
  63. Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B. 63.  2011. Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res. 39:9155–66 [Google Scholar]
  64. Skiniotis G, Moazed D, Walz T. 64.  2007. Acetylated histone tail peptides induce structural rearrangements in the RSC chromatin remodeling complex. J. Biol. Chem. 282:20804–8 [Google Scholar]
  65. Hassan AH, Neely KE, Workman JL. 65.  2001. Histone acetyltransferase complexes stabilize swi/snf binding to promoter nucleosomes. Cell 104:817–27 [Google Scholar]
  66. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M. 66.  et al. 2002. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369–79 [Google Scholar]
  67. Kasten M, Szerlong H, Erdjument-Bromage H, Tempst P, Werner M, Cairns BR. 67.  2004. Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J. 23:1348–59 [Google Scholar]
  68. VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns BR. 68.  2007. Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol. Cell 27:817–28 [Google Scholar]
  69. Sen P, Ghosh P, Pugh BF, Bartholomew B. 69.  2011. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Res. 39:9155–66 [Google Scholar]
  70. Sen P, Vivas P, Dechassa ML, Mooney AM, Poirier MG, Bartholomew B. 70.  2013. The SnAC domain of SWI/SNF is a histone anchor required for remodeling. Mol. Cell. Biol. 33:360–70 [Google Scholar]
  71. Lavigne M, Eskeland R, Azebi S, Saint-André V, Jang SM. 71.  et al. 2009. Interaction of HP1 and Brg1/Brm with the globular domain of histone H3 is required for HP1-mediated repression. PLoS Genet. 5:e1000769 [Google Scholar]
  72. Wu WH, Alami S, Luk E, Wu CH, Sen S. 72.  et al. 2005. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol. 12:1064–71 [Google Scholar]
  73. Wu WH, Wu CH, Ladurner A, Mizuguchi G, Wei D. 73.  et al. 2009. N terminus of Swr1 binds to histone H2AZ and provides a platform for subunit assembly in the chromatin remodeling complex. J. Biol. Chem. 284:6200–7 [Google Scholar]
  74. Gangaraju VK, Bartholomew B. 74.  2007. Dependency of ISW1a chromatin remodeling on extranucleosomal DNA. Mol. Cell. Biol. 27:3217–25 [Google Scholar]
  75. Kagalwala MN, Glaus BJ, Dang W, Zofall M, Bartholomew B. 75.  2004. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23:2092–104 [Google Scholar]
  76. Boyer LA, Latek RR, Peterson CL. 76.  2004. The SANT domain: a unique histone-tail-binding module?. Nat. Rev. Mol. Cell. Biol. 5:158–63 [Google Scholar]
  77. Grüne T, Brzeski J, Eberharter A, Clapier CR, Corona DF. 77.  et al. 2003. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12:449–60 [Google Scholar]
  78. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C. 78.  et al. 2011. Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 472:448–53 [Google Scholar]
  79. Ryan DP, Sundramoorthy R, Martin D, Singh V, Owen-Hughes T. 79.  2011. The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J. 30:2596–609 [Google Scholar]
  80. Sharma A, Jenkins KR, Heroux A, Bowman GD. 80.  2011. Crystal structure of the chromo-helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J. Biol. Chem. 286:42099–104 [Google Scholar]
  81. Mueller-Planitz F, Klinker H, Ludwigsen J, Becker PB. 81.  2013. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat. Struct. Mol. Biol. 20:82–89 [Google Scholar]
  82. Clapier CR, Cairns BR. 82.  2012. Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492:280–84 [Google Scholar]
  83. McKnight JN, Jenkins KR, Nodelman IM, Escobar T, Bowman GD. 83.  2011. Extranucleosomal DNA binding directs nucleosome sliding by Chd1. Mol. Cell. Biol. 31:4746–59 [Google Scholar]
  84. Patel A, Chakravarthy S, Morrone S, Nodelman IM, McKnight JM, Bowman GD. 84.  2013. Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler. Nucleic Acids Res. 41:1637–48 [Google Scholar]
  85. Udugama M, Sabri A, Bartholomew B. 85.  2010. The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor. Mol. Cell. Biol. 31:662–73 [Google Scholar]
  86. Kapoor P, Chen M, Winkler DD, Luger K, Shen X. 86.  2013. Evidence for monomeric actin function in INO80 chromatin remodeling. Nat. Struct. Mol. Biol. 20:426–32 [Google Scholar]
  87. Gerhold CB, Winkler DD, Lakomek K, Seifert FU, Fenn S. 87.  et al. 2012. Structure of actin-related protein 8 and its contribution to nucleosome binding. Nucleic Acids Res. 40:11036–46 [Google Scholar]
  88. Bartholomew B.88.  2013. Monomeric actin required for INO80 remodeling. Nat. Struct. Mol. Biol. 20:405–7 [Google Scholar]
  89. Singh M, D'Silva L, Holak TA. 89.  2006. DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein. Biol. Chem. 387:1469–78 [Google Scholar]
  90. Aravind L, Landsman D. 90.  1998. AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 26:4413–21 [Google Scholar]
  91. Wilsker D, Patsialou A, Dallas PB, Moran E. 91.  2002. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13:95–106 [Google Scholar]
  92. Wilsker D, Probst L, Wain HM, Maltais L, Tucker PW, Moran E. 92.  2005. Nomenclature of the ARID family of DNA-binding proteins. Genomics 86:242–51 [Google Scholar]
  93. Wang T, Zhang J, Zhang X, Tu X. 93.  2012. Solution structure of SWI1 AT-rich interaction domain from Saccharomyces cerevisiae and its nonspecific binding to DNA. Proteins 80:1911–17 [Google Scholar]
  94. Wilsker D, Patsialou A, Zumbrun SD, Kim S, Chen Y. 94.  et al. 2004. The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes. Nucleic Acids Res. 32:1345–53 [Google Scholar]
  95. Aravind L, Iyer LM. 95.  2002. The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol. 3:research0039 [Google Scholar]
  96. Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R. 96.  2006. Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc. Natl. Acad. Sci. USA 103:2057–62 [Google Scholar]
  97. Qian C, Zhang Q, Li S, Zeng L, Walsh MJ, Zhou MM. 97.  2005. Structure and chromosomal DNA binding of the SWIRM domain. Nat. Struct. Mol. Biol. 12:1078–85 [Google Scholar]
  98. Chandler RL, Brennan J, Schisler JC, Serber D, Patterson C, Magnuson T. 98.  2013. ARID1a–DNA interactions are required for promoter occupancy by SWI/SNF. Mol. Cell. Biol. 33:265–80 [Google Scholar]
  99. Yoneyama M, Tochio N, Umehara T, Koshiba S, Inoue M. 99.  et al. 2007. Structural and functional differences of SWIRM domain subtypes. J. Mol. Biol. 369:222–38 [Google Scholar]
  100. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. 100.  2002. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res. 12:47–56 [Google Scholar]
  101. Shen X, Ranallo R, Choi C, Wu C. 101.  2003. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol. Cell 12:147–55 [Google Scholar]
  102. Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC. 102.  et al. 2013. Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc. Natl. Acad. Sci. USA 110:3345–50 [Google Scholar]
  103. Fenn Breitsprecher S D, Gerhold CB, Witte G, Faix J, Hopfner KP. 103.  2011. Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin. EMBO J. 30:2153–66 [Google Scholar]
  104. Cairns BR, Erdjument-Bromage H, Tempst P, Winston F, Kornberg RD. 104.  1998. Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol. Cell 2:639–51 [Google Scholar]
  105. Jha S, Dutta A. 105.  2009. RVB1/RVB2: running rings around molecular biology. Mol. Cell 34:521–33 [Google Scholar]
  106. Nano N, Houry WA. 106.  2013. Chaperone-like activity of the AAA+ proteins Rvb1 and Rvb2 in the assembly of various complexes. Philos. Trans. R. Soc. B 368:20110399 [Google Scholar]
  107. Jónsson ZO, Jha S, Wohlschlegel JA, Dutta A. 107.  2004. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 16:465–77 [Google Scholar]
  108. Davey CA, Sargent DF, Luger J, Mäder AW, Richmond TJ. 108.  2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319:1097–113 [Google Scholar]
  109. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 109.  1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–60 [Google Scholar]
  110. Flaus A, Owen-Hughes T. 110.  2004. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?. Curr. Opin. Genet. Dev. 14:165–73 [Google Scholar]
  111. Bowman GD.111.  2010. Mechanisms of ATP-dependent nucleosome sliding. Curr. Opin. Struct. Biol. 20:73–81 [Google Scholar]
  112. Flaus A, Owen-Hughes T. 112.  2003. Mechanisms for nucleosome mobilization. Biopolymers 68:563–78 [Google Scholar]
  113. Ong MS, Richmond TJ, Davey CA. 113.  2007. DNA stretching and extreme kinking in the nucleosome core. J. Mol. Biol. 368:1067–74 [Google Scholar]
  114. Aoyagi S, Hayes JJ. 114.  2002. hSWI/SNF-catalyzed nucleosome sliding does not occur solely via a twist-diffusion mechanism. Mol. Cell. Biol. 22:7484–90 [Google Scholar]
  115. Strohner R, Wachsmuth M, Dachauer K, Mazurkiewicz J, Hochstadter J. 115.  et al. 2005. A “loop recapture” mechanism for ACF-dependent nucleosome remodeling. Nat. Struct. Mol. Biol. 12:683–90 [Google Scholar]
  116. Lorch Y, Davis B, Kornberg RD. 116.  2005. Chromatin remodeling by DNA bending, not twisting. Proc. Natl. Acad. Sci. USA 102:1329–32 [Google Scholar]
  117. Langst G, Becker PB. 117.  2001. ISWI induces nucleosome sliding on nicked DNA. Mol. Cell 8:1085–92 [Google Scholar]
  118. Narlikar GJ, Phelan ML, Kingston RE. 118.  2001. Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Mol. Cell 8:1219–30 [Google Scholar]
  119. Fan HY, He X, Kingson RE, Narlikar GJ. 119.  2003. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell 11:1311–22 [Google Scholar]
  120. Liu N, Peterson CL, Hayes JJ. 120.  2011. SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol. Cell. Biol. 31:4165–75 [Google Scholar]
  121. Narlikar GJ, Sundaramoorthy R, Owen-Hughes T. 121.  2013. Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes. Cell 154:490–503 [Google Scholar]
  122. Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC. 122.  et al. 2006. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21:417–25 [Google Scholar]
  123. Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. 123.  2011. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J. 30:2364–72 [Google Scholar]
  124. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S. 124.  et al. 2006. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24:559–68 [Google Scholar]
  125. Kassabov SR, Zhang B, Persinger J, Bartholomew B. 125.  2003. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell 11:391–403 [Google Scholar]
  126. Cote J, Peterson CL, Workman JL. 126.  1998. Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. USA 95:4947–52 [Google Scholar]
  127. Kassabov SR, Henry NM, Zofall M, Tsukiyama T, Bartholomew B. 127.  2002. High-resolution mapping of changes in histone–DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:7524–34 [Google Scholar]
  128. Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL. 128.  et al. 2007. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell 128:1003–12 [Google Scholar]
  129. Racki LR, Narlikar GJ. 129.  2008. ATP-dependent chromatin remodeling enzymes: Two heads are not better, just different. Curr. Opin. Genet. Dev. 18:137–44 [Google Scholar]
  130. Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A. 130.  et al. 2009. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462:1016–21 [Google Scholar]
  131. Gangaraju VK, Prasad P, Srour A, Kagalwala MN, Bartholomew B. 131.  2009. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol. Cell 35:58–69 [Google Scholar]
  132. Erdel F, Schubert T, Marth C, Längst G, Rippe K. 132.  2010. Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc. Natl. Acad. Sci. USA 107:19873–78 [Google Scholar]
  133. Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, Längst G. 133.  2007. DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc. Natl. Acad. Sci. USA 104:15635–40 [Google Scholar]
  134. Yang JG, Madrid TS, Sevastopoulos E, Narlihar GJ. 134.  2006. The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nat. Struct. Mol. Biol. 13:1078–83 [Google Scholar]
  135. Dang W, Kagalwala MN, Bartholomew B. 135.  2006. Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Mol. Cell. Biol. 26:7388–96 [Google Scholar]
  136. Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C. 136.  1999. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:686–97 [Google Scholar]
  137. Vary JC Jr, Gangaraju VJ, Qin J, Landel CC, Kooperberg C. 137.  et al. 2003. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23:80–91 [Google Scholar]
  138. Engeholm M, de Jager M, Flaus A, Brenk R, van Noort J, Owen-Hughes T. 138.  2009. Nucleosomes can invade DNA territories occupied by their neighbors. Nat. Struct. Mol. Biol. 16:151–58 [Google Scholar]
  139. Chaban Y, Ezeokonkwo C, Chung W-H, Zhang F, Kornberg RD. 139.  et al. 2008. Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat. Struct. Mol. Biol. 15:1272–77 [Google Scholar]
  140. Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C. 140.  et al. 2007. Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc. Natl. Acad. Sci. USA 104:4913–18 [Google Scholar]
  141. Gkikopoulos T, Havas KM, Dewar J, Owen-Hughes T. 141.  2009. SWI/SNF and Asf1p cooperate to displace histones during induction of the Saccharomyces cerevisiae HO promoter. Mol. Cell. Biol. 29:4057–66 [Google Scholar]
  142. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. 142.  2003. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11:1587–98 [Google Scholar]
  143. Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD. 143.  2010. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev 24:1758–71 [Google Scholar]
  144. Lorch Y, Maier-Davis B, Kornberg RD. 144.  2006. Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl. Acad. Sci. USA 103:3090–93 [Google Scholar]
  145. Wippo CJ, Israel L, Watanabe S, Hochheimer A, Peterson CL, Korber P. 145.  2011. The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J. 30:1277–88 [Google Scholar]
  146. Corona DF, Clapier CR, Becker PB, Tamkun JW. 146.  2002. Modulation of ISWI function by site-specific histone acetylation. EMBO Rep. 3:242–47 [Google Scholar]
  147. Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. 147.  2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–47 [Google Scholar]
  148. Smith CL, Peterson CL. 148.  2005. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol. Cell. Biol. 25:5880–92 [Google Scholar]
  149. Hsu DS, Kim ST, Sun Q, Sancar A. 149.  1995. Structure and function of the UvrB protein. J. Biol. Chem. 270:8319–27 [Google Scholar]
  150. Moolenaar GF, Visse R, Ortiz-Buysse M, Goosen N, van de Putte P. 150.  1994. Helicase motifs V and VI of the Escherichia coli UvrB protein of the UvrABC endonuclease are essential for the formation of the preincision complex. J. Mol. Biol. 240:294–307 [Google Scholar]
  151. Patel A, McKnight JN, Genzor P, Bowman GD. 151.  2011. Identification of residues in chromo-helicase DNA-binding protein 1 (Chd1) required for coupling ATP hydrolysis to nucleosome sliding. J. Biol. Chem. 286:43984–93 [Google Scholar]
  152. Kadam S, McAlpine GS, Phelan ML, Kingson RE, Jones KA, Emerson BM. 152.  2000. Functional selectivity of recombinant mammalian SWI/SNF subunits. Genes Dev. 14:2441–51 [Google Scholar]
  153. Phelan ML, Sif S, Narlikar GJ, Kingson RE. 153.  1999. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3:247–53 [Google Scholar]
  154. He X, Fan HY, Narlikar GJ, Kingson RE. 154.  2006. Human ACF1 alters the remodeling strategy of SNF2h. J. Biol. Chem. 281:28636–47 [Google Scholar]
  155. He X, Fan HY, Garlick JD, Kingston RE. 155.  2008. Diverse regulation of SNF2h chromatin remodeling by noncatalytic subunits. Biochemistry 47:7025–33 [Google Scholar]
  156. Staahl BT, Tiang J, Wu W, Sun A, Gitler AD. 156.  2013. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. J. Neurosci. 33:10348–61 [Google Scholar]
  157. Vogel-Ciernia A, Matheos DP, Barrett RM, Kramár EA, Azzawi S. 157.  et al. 2013. The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat. Neurosci. 16:552–61 [Google Scholar]
  158. Romero OA, Sanchez-Cespedes M. 158.  2013. The SWI/SNF genetic blockade: effects in cell differentiation, cancer and developmental diseases. Oncogene In press [Google Scholar]
  159. Shain AH, Pollack JR. 159.  2013. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS ONE 8:e55119 [Google Scholar]
  160. Sif S, Stukenberg PT, Kirschner MW, Kingson RE. 160.  1998. Mitotic inactivation of a human SWI/SNF chromatin remodeling complex. Genes Dev. 12:2842–51 [Google Scholar]
  161. Muchardt C, Reyes JC, Bourachot B, Leguoy E, Yaniv M. 161.  1996. The hbrm and BRG-1 proteins, components of the human SNF/SWI complex, are phosphorylated and excluded from the condensed chromosomes during mitosis. EMBO J. 15:3394–402 [Google Scholar]
  162. Kim JH, Saraf A, Florens L, Washburn M, Workman JL. 162.  2010. Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2. Genes Dev. 24:2766–71 [Google Scholar]
  163. Zhang Y, Cheng MB, Zhang YJ, Zhong X, Dai H. 163.  et al. 2010. A switch from hBrm to Brg1 at IFNγ-activated sequences mediates the activation of human genes. Cell Res. 20:1345–60 [Google Scholar]
  164. Ferreira R, Eberharter A, Bonaldi T, Chioda M, Imhof A, Becker PB. 164.  2007. Site-specific acetylation of ISWI by GCN5. BMC Mol. Biol. 8:73 [Google Scholar]
  165. Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. 165.  2009. Dynamics of nucleosome remodeling by individual ACF complexes. Nature 462:1022–27 [Google Scholar]
/content/journals/10.1146/annurev-biochem-051810-093157
Loading
/content/journals/10.1146/annurev-biochem-051810-093157
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error