Regulated nucleosome mobility and the histone code
10.1038/nsmb851
Crossref journal-article
Springer Science and Business Media LLC
Nature Structural & Molecular Biology (297)
Bibliography

Cosgrove, M. S., Boeke, J. D., & Wolberger, C. (2004). Regulated nucleosome mobility and the histone code. Nature Structural & Molecular Biology, 11(11), 1037–1043.

Authors 3
  1. Michael S Cosgrove (first)
  2. Jef D Boeke (additional)
  3. Cynthia Wolberger (additional)
References 73 Referenced 304
  1. Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002). (10.1016/S0092-8674(02)00654-2) / Cell by GJ Narlikar (2002)
  2. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000). (10.1038/47412) / Nature by BD Strahl (2000)
  3. Fischle, W., Wang, Y. & Allis, C.D. Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475–479 (2003). (10.1038/nature02017) / Nature by W Fischle (2003)
  4. Cocklin, R.R. & Wang, M. Identification of methylation and acetylation sites on mouse histone H3 using matrix-assisted laser desorption/ionization time-of-flight and nanoelectrospray ionization tandem mass spectrometry. J. Protein Chem. 22, 327–334 (2003). (10.1023/A:1025334006014) / J. Protein Chem. by RR Cocklin (2003)
  5. Zhang, K. et al. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal. Biochem. 306 259–269 (2002). (10.1006/abio.2002.5719) / Anal. Biochem. by K Zhang (2002)
  6. Zhang, L., Eugeni, E.E., Parthun, M.R. & Freitas, M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112, 77–86 (2003). (10.1007/s00412-003-0244-6) / Chromosoma by L Zhang (2003)
  7. Freitas, M.A., Sklenar, A.R. & Parthun, M.R. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell Biochem. 92, 691–700 (2004). (10.1002/jcb.20106) / J. Cell Biochem. by MA Freitas (2004)
  8. Hansen, J.C. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31, 361–392 (2002). (10.1146/annurev.biophys.31.101101.140858) / Annu. Rev. Biophys. Biomol. Struct. by JC Hansen (2002)
  9. Luger, K. Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev. 13, 127–135 (2003). (10.1016/S0959-437X(03)00026-1) / Curr. Opin. Genet. Dev. by K Luger (2003)
  10. Pennings, S., Meersseman, G. & Bradbury, E.M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220, 101–110 (1991). (10.1016/0022-2836(91)90384-I) / J. Mol. Biol. by S Pennings (1991)
  11. Becker, P.B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273 (2002). (10.1146/annurev.biochem.71.110601.135400) / Annu. Rev. Biochem. by PB Becker (2002)
  12. Becker, P.B. Nucleosome sliding: facts and fiction. EMBO J. 21, 4749–4753 (2002). (10.1093/emboj/cdf486) / EMBO J. by PB Becker (2002)
  13. Eisen, J.A., Sweder, K.S. & Hanawalt, P.C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23, 2715–2723 (1995). (10.1093/nar/23.14.2715) / Nucleic Acids Res. by JA Eisen (1995)
  14. Whitehouse, I. et al. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400, 784–787 (1999). (10.1038/23506) / Nature by I Whitehouse (1999)
  15. Langst, G. & Becker, P.B. ISWI induces nucleosome sliding on nicked DNA. Mol. Cell 8, 1085–1092 (2001). (10.1016/S1097-2765(01)00397-5) / Mol. Cell by G Langst (2001)
  16. Guschin, D. & Wolffe, A.P. SWItched-on mobility. Curr. Biol. 9, R742–R746 (1999). (10.1016/S0960-9822(99)80473-4) / Curr. Biol. by D Guschin (1999)
  17. Schnitzler, G., Sif, S. & Kingston, R.E. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 94, 17–27 (1998). (10.1016/S0092-8674(00)81217-9) / Cell by G Schnitzler (1998)
  18. Lorch, Y., Cairns, B.R., Zhang, M. & Kornberg, R.D. Activated RSC–nucleosome complex and persistently altered form of the nucleosome. Cell 94, 29–34 (1998). (10.1016/S0092-8674(00)81218-0) / Cell by Y Lorch (1998)
  19. Imbalzano, A.N., Schnitzler, G.R. & Kingston, R.E. Nucleosome disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis. J. Biol. Chem. 271, 20726–20733 (1996). (10.1074/jbc.271.34.20726) / J. Biol. Chem. by AN Imbalzano (1996)
  20. Cote, J., Peterson, C.L. & Workman, J.L. 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, 4947–4952 (1998). (10.1073/pnas.95.9.4947) / Proc. Natl. Acad. Sci. USA by J Cote (1998)
  21. Owen-Hughes, T., Utley, R.T., Cote, J., Peterson, C.L. & Workman, J.L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273, 513–516 (1996). (10.1126/science.273.5274.513) / Science by T Owen-Hughes (1996)
  22. Bazett-Jones, D.P., Cote, J., Landel, C.C., Peterson, C.L. & Workman, J.L. The SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains. Mol. Cell. Biol. 19, 1470–1478 (1999). (10.1128/MCB.19.2.1470) / Mol. Cell. Biol. by DP Bazett-Jones (1999)
  23. Zeng, L. & Zhou, M.M. Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513, 124–128 (2002). (10.1016/S0014-5793(01)03309-9) / FEBS Lett. by L Zeng (2002)
  24. Brehm, A., Tufteland, K.R., Aasland, R. & Becker, P.B. The many colours of chromodomains. Bioessays 26, 133–140 (2004). (10.1002/bies.10392) / Bioessays by A Brehm (2004)
  25. White, C.L., Suto, R.K. & Luger, K. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20, 5207–5218 (2001). (10.1093/emboj/20.18.5207) / EMBO J. by CL White (2001)
  26. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. & Richmond, T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319, 1097–1113 (2002). (10.1016/S0022-2836(02)00386-8) / J. Mol. Biol. by CA Davey (2002)
  27. Cuthbert, G.L. et al. Histone deimination antagonizes arginine methylation. Cell 118, 545–553 (2004). (10.1016/j.cell.2004.08.020) / Cell by GL Cuthbert (2004)
  28. Wang, Y. et al. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306, 279–283 (2004). (10.1126/science.1101400) / Science by Y Wang (2004)
  29. Roberts, S.M. & Winston, F. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147, 451–465 (1997). (10.1093/genetics/147.2.451) / Genetics by SM Roberts (1997)
  30. Pollard, K.J. & Peterson, C.L. Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol. Cell. Biol. 17, 6212–6222 (1997). (10.1128/MCB.17.11.6212) / Mol. Cell. Biol. by KJ Pollard (1997)
  31. Syntichaki, P., Topalidou, I. & Thireos, G. The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature 404, 414–417 (2000). (10.1038/35006136) / Nature by P Syntichaki (2000)
  32. Brownell, J.E. et al. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843–851 (1996). (10.1016/S0092-8674(00)81063-6) / Cell by JE Brownell (1996)
  33. Guyon, J.R., Narlikar, G.J., Sif, S. & Kingston, R.E. Stable remodeling of tailless nucleosomes by the human SWI–SNF complex. Mol. Cell. Biol. 19, 2088–2097 (1999). (10.1128/MCB.19.3.2088) / Mol. Cell. Biol. by JR Guyon (1999)
  34. Park, J.H., Cosgrove, M.S., Youngman, E., Wolberger, C. & Boeke, J.D. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32, 273–279 (2002). (10.1038/ng982) / Nat. Genet. by JH Park (2002)
  35. Kruger, W. et al. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 9, 2770–2779 (1995). (10.1101/gad.9.22.2770) / Genes Dev. by W Kruger (1995)
  36. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260 (1997). (10.1038/38444) / Nature by K Luger (1997)
  37. Perez-Martin, J. & Johnson, A.D. Mutations in chromatin components suppress a defect of Gcn5 protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 1049–1054 (1998). (10.1128/MCB.18.2.1049) / Mol. Cell. Biol. by J Perez-Martin (1998)
  38. Muthurajan, U.M. et al. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23, 260–271 (2004). (10.1038/sj.emboj.7600046) / EMBO J. by UM Muthurajan (2004)
  39. Flaus, A., Rencurel, C., Ferreira, H., Wiechens, N. & Owen-Hughes, T. Sin mutations alter inherent nucleosome mobility. EMBO J. 23, 343–353 (2004). (10.1038/sj.emboj.7600047) / EMBO J. by A Flaus (2004)
  40. Kadosh, D. & Struhl, K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89, 365–371 (1997). (10.1016/S0092-8674(00)80217-2) / Cell by D Kadosh (1997)
  41. Horn, P.J., Crowley, K.A., Carruthers, L.M., Hansen, J.C. & Peterson, C.L. The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arrays. Nat. Struct. Biol. 9, 167–171 (2002). (10.1038/nsb776) / Nat. Struct. Biol. by PJ Horn (2002)
  42. Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R. & O'Shea, E.K. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114–116 (2003). (10.1126/science.1078062) / Science by DJ Steger (2003)
  43. Shen, X., Xiao, H., Ranallo, R., Wu, W.H. & Wu, C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science 299, 112–114 (2003). (10.1126/science.1078068) / Science by X Shen (2003)
  44. Kruger, W. & Herskowitz, I. A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol. Cell. Biol. 11, 4135–4146 (1991). (10.1128/MCB.11.8.4135) / Mol. Cell. Biol. by W Kruger (1991)
  45. Mizuguchi, G. et al. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303, 343–348 (2004). (10.1126/science.1090701) / Science by G Mizuguchi (2004)
  46. Redon, C. et al. Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12, 162–169 (2002). (10.1016/S0959-437X(02)00282-4) / Curr. Opin. Genet. Dev. by C Redon (2002)
  47. McKittrick, E., Gafken, P.R., Ahmad, K. & Henikoff, S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. USA 101, 1525–1530 (2004). (10.1073/pnas.0308092100) / Proc. Natl. Acad. Sci. USA by E McKittrick (2004)
  48. Noma, K., Allis, C.D. & Grewal, S.I. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150–1155 (2001). (10.1126/science.1064150) / Science by K Noma (2001)
  49. Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T.J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327, 85–96 (2003). (10.1016/S0022-2836(03)00025-1) / J. Mol. Biol. by B Dorigo (2003)
  50. Clapier, C.R., Nightingale, K.P. & Becker, P.B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30, 649–655 (2002). (10.1093/nar/30.3.649) / Nucleic Acids Res. by CR Clapier (2002)
  51. Hamiche, A., Kang, J.G., Dennis, C., Xiao, H. & Wu, C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. USA 98, 14316–14321 (2001). (10.1073/pnas.251421398) / Proc. Natl. Acad. Sci. USA by A Hamiche (2001)
  52. Clapier, C.R., Langst, G., Corona, D.F., Becker, P.B. & Nightingale, K.P. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21, 875–883 (2001). (10.1128/MCB.21.3.875-883.2001) / Mol. Cell. Biol. by CR Clapier (2001)
  53. Langst, G. & Becker, P.B. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58–63 (2004). (10.1016/j.bbaexp.2003.10.011) / Biochim. Biophys. Acta by G Langst (2004)
  54. Hassan, A.H. et al. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111, 369–379 (2002). (10.1016/S0092-8674(02)01005-X) / Cell by AH Hassan (2002)
  55. Kasten, M. et al. Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J. 23, 1348–1359 (2004). (10.1038/sj.emboj.7600143) / EMBO J. by M Kasten (2004)
  56. Nishioka, K. et al. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev. 16, 479–489 (2002). (10.1101/gad.967202) / Genes Dev. by K Nishioka (2002)
  57. Ahringer, J. NuRD and SIN3 histone deacetylase complexes in development. Trends Genet. 16, 351–356 (2000). (10.1016/S0168-9525(00)02066-7) / Trends Genet. by J Ahringer (2000)
  58. van Leeuwen, F., Gafken, P.R. & Gottschling, D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109, 745–756 (2002). (10.1016/S0092-8674(02)00759-6) / Cell by F van Leeuwen (2002)
  59. Li, G. & Widom, J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763–769 (2004). (10.1038/nsmb801) / Nat. Struct. Mol. Biol. by G Li (2004)
  60. Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259–272 (2004). (10.1016/S0092-8674(04)00044-3) / Cell by S Khorasanizadeh (2004)
  61. Fleming, A.B. & Pennings, S. Antagonistic remodelling by Swi-Snf and Tup1-Ssn6 of an extensive chromatin region forms the background for FLO1 gene regulation. EMBO J. 20, 5219–5231 (2001). (10.1093/emboj/20.18.5219) / EMBO J. by AB Fleming (2001)
  62. Maile, T., Kwoczynski, S., Katzenberger, R.J., Wassarman, D.A. & Sauer, F. TAF1 activates transcription by phosphorylation of serine 33 in histone H2B. Science 304, 1010–1014 (2004). (10.1126/science.1095001) / Science by T Maile (2004)
  63. Sun, Z.W. & Allis, C.D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418, 104–108 (2002). (10.1038/nature00883) / Nature by ZW Sun (2002)
  64. Ng, H.H., Xu, R.M., Zhang, Y. & Struhl, K. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J. Biol. Chem. 277, 34655–34657 (2002). (10.1074/jbc.C200433200) / J. Biol. Chem. by HH Ng (2002)
  65. Briggs, S.D. et al. Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418, 498 (2002). (10.1038/nature00970) / Nature by SD Briggs (2002)
  66. DiRenzo, J. et al. BRG-1 is recruited to estrogen-responsive promoters and cooperates with factors involved in histone acetylation. Mol. Cell. Biol. 20, 7541–7549 (2000). (10.1128/MCB.20.20.7541-7549.2000) / Mol. Cell. Biol. by J DiRenzo (2000)
  67. Mizuguchi, G., Vassilev, A., Tsukiyama, T., Nakatani, Y. & Wu, C. ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J. Biol. Chem. 276, 14773–14783 (2001). (10.1074/jbc.M100125200) / J. Biol. Chem. by G Mizuguchi (2001)
  68. Galarneau, L. et al. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5, 927–937 (2000). (10.1016/S1097-2765(00)80258-0) / Mol. Cell by L Galarneau (2000)
  69. Reid, J.L., Iyer, V.R., Brown, P.O. & Struhl, K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6, 1297–1307 (2000). (10.1016/S1097-2765(00)00128-3) / Mol. Cell by JL Reid (2000)
  70. Kim, J. et al. Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10, 345–355 (1999). (10.1016/S1074-7613(00)80034-5) / Immunity by J Kim (1999)
  71. Fazzio, T.G. et al. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21, 6450–6460 (2001). (10.1128/MCB.21.19.6450-6460.2001) / Mol. Cell. Biol. by TG Fazzio (2001)
  72. Sif, S., Saurin, A.J., Imbalzano, A.N. & Kingston, R.E. Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev. 15, 603–618 (2001). (10.1101/gad.872801) / Genes Dev. by S Sif (2001)
  73. Zhou, Y., Santoro, R. & Grummt, I. The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J. 21, 4632–4640 (2002). (10.1093/emboj/cdf460) / EMBO J. by Y Zhou (2002)
Dates
Type When
Created 20 years, 9 months ago (Nov. 2, 2004, 2:43 p.m.)
Deposited 2 years, 3 months ago (May 19, 2023, 12:54 a.m.)
Indexed 6 days, 4 hours ago (Aug. 21, 2025, 1:15 p.m.)
Issued 20 years, 9 months ago (Nov. 1, 2004)
Published 20 years, 9 months ago (Nov. 1, 2004)
Published Online 20 years, 9 months ago (Nov. 2, 2004)
Published Print 20 years, 9 months ago (Nov. 1, 2004)
Funders 0

None

@article{Cosgrove_2004, title={Regulated nucleosome mobility and the histone code}, volume={11}, ISSN={1545-9985}, url={http://dx.doi.org/10.1038/nsmb851}, DOI={10.1038/nsmb851}, number={11}, journal={Nature Structural & Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Cosgrove, Michael S and Boeke, Jef D and Wolberger, Cynthia}, year={2004}, month=nov, pages={1037–1043} }