Skip to main content
SpringerLink
Log in

Control of Nucleosome Positions by DNA Sequence and Remodeling Machines

  • Original Paper
  • Published:
Cell Biochemistry and Biophysics Aims and scope Submit manuscript

Abstract

Recent studies have shown that promoter nucleosomes frequently adopt specific positions, and indicate that these positions functionally regulate transcription factor binding. Other studies indicate that DNA sequence has a major role in establishing these nucleosome positions, suggesting that evolution has selected for specific, default arrangements of promoter nucleosomes. Finally, recent studies indicate that ATP-dependent chromatin remodeling complexes move nucleosomes away from default positioning sequences, either to complex-preferred locations or to establish a complex-preferred spacing between nucleosomes. Here we will review these recent findings, and consider how combinations of promoter sequence and specific remodeling complexes may act to switch chromatin between permissive and repressive conformations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Gottesfeld, J. M., & Luger, K. (2001). Energetics and affinity of the histone octamer for defined DNA sequences. Biochemistry, 40, 10927–10933.

    PubMed  CAS  Google Scholar 

  2. Beato, M., & Eisfeld, K. (1997). Transcription factor access to chromatin. Nucleic Acids Research, 25, 3559–3563.

    PubMed  CAS  Google Scholar 

  3. Kwon, J., Imbalzano, A. N., Matthews, A., & Oettinger, M. A. (1998). Accessibility of nucleosomal DNA to V(D)J cleavage is modulated by RSS positioning and HMG1. Molecular Cell, 2, 829–839.

    PubMed  CAS  Google Scholar 

  4. Adams, C. C., & Workman, J. L. (1995). Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Molecular and Cellular Biology, 15, 1405–1421.

    PubMed  CAS  Google Scholar 

  5. Polach, K. J., & Widom, J. (1996). A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. Journal of Molecular Biology, 258, 800–812.

    PubMed  CAS  Google Scholar 

  6. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389, 251–260.

    PubMed  CAS  Google Scholar 

  7. Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I. K., et al. (2006). A genomic code for nucleosome positioning. Nature, 442, 772–778.

    PubMed  CAS  Google Scholar 

  8. Satchwell, S. C., Drew, H. R., & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology, 191, 659–675.

    PubMed  CAS  Google Scholar 

  9. Widlund, H. R., Cao, H., Simonsson, S., Magnusson, E., Simonsson, T., Nielsen, P. E., et al. (1997). Identification and characterization of genomic nucleosome-positioning sequences. Journal of Molecular Biology, 267, 807–817.

    PubMed  CAS  Google Scholar 

  10. Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., & Trifonov, E. N. (1996). Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. Journal of Molecular Biology, 262, 129–139.

    PubMed  CAS  Google Scholar 

  11. Ioshikhes, I. P., Albert, I., Zanton, S. J., & Pugh, B. F. (2006). Nucleosome positions predicted through comparative genomics. Nature Genetics, 38, 1210–1215.

    PubMed  CAS  Google Scholar 

  12. Yuan, G. C., Liu, Y. J., Dion, M. F., Slack, M. D., Wu, L. F., Altschuler, S. J., et al. (2005). Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626–630.

    PubMed  CAS  Google Scholar 

  13. Albert, I., Mavrich, T. N., Tomsho, L. P., Qi, J., Zanton, S. J., Schuster, S. C., et al. (2007). Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446, 572–576.

    PubMed  CAS  Google Scholar 

  14. Ozsolak, F., Song, J. S., Liu, X. S., & Fisher, D. E. (2007). High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology, 25, 244–248.

    PubMed  CAS  Google Scholar 

  15. Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., et al. (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell, 132, 887–898.

    PubMed  CAS  Google Scholar 

  16. Roberts, M. S., Fragoso, G., & Hager, G. L. (1995). Nucleosomes reconstituted in vitro on mouse mammary tumor virus B region DNA occupy multiple translational and rotational frames. Biochemistry, 34, 12470–12480.

    PubMed  CAS  Google Scholar 

  17. Costanzo, G., Di Mauro, E., Negri, R., Pereira, G., & Hollenberg, C. (1995). Multiple overlapping positions of nucleosomes with single in vivo rotational setting in the Hansenula polymorpha RNA polymerase II MOX promoter. Journal of Biological Chemistry, 270, 11091–11097.

    PubMed  CAS  Google Scholar 

  18. Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., et al. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99–104.

    PubMed  CAS  Google Scholar 

  19. Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., et al. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799–804.

    PubMed  CAS  Google Scholar 

  20. Sekinger, E. A. M., Moqtaderi, Z., & Struhl, K. (2005). Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Molecular Cell, 18, 735–748.

    PubMed  CAS  Google Scholar 

  21. Morohashi, N., Yamamoto, Y., Kuwana, S., Morita, W., Shindo, H., Mitchell, A. P., et al. (2006). Effect of Sequence-Directed Nucleosome Disruption on Cell-Type-Specific Repression by {alpha}2/Mcm1 in the Yeast Genome. Eukaryotic Cell, 5, 1925–1933.

    PubMed  CAS  Google Scholar 

  22. Lomvardas, S., & Thanos, D. (2002). Modifying gene expression programs by altering core promoter chromatin architecture. Cell, 110, 261–271.

    PubMed  CAS  Google Scholar 

  23. Tabancay, A. P., Jr., & Forsburg, S. L. (2006). Eukaryotic DNA replication in a chromatin context. Current Topics in Developmental Biology, 76, 129–184.

    PubMed  CAS  Google Scholar 

  24. Zlatanova, J., Seebart, C., & Tomschik, M. (2007). Nap1: taking a closer look at a juggler protein of extraordinary skills. FASEB Journal, 21, 1294–1310.

    PubMed  CAS  Google Scholar 

  25. Terrell, A. R., Wongwisansri, S., Pilon, J. L., & Laybourn, P. J. (2002). Reconstitution of nucleosome positioning, remodeling, histone acetylation, and transcriptional activation on the PHO5 promoter. Journal of Biological Chemistry, 277, 31038–31047.

    PubMed  CAS  Google Scholar 

  26. Meersseman, G., Pennings, S., & Bradbury, E. M. (1992). Mobile nucleosomes–a general behavior. EMBO Journal, 11, 2951–2959.

    PubMed  CAS  Google Scholar 

  27. Sera, T., & Wolffe, A. P. (1998). Role of histone H1 as an architectural determinant of chromatin structure and as a specific repressor of transcription on Xenopus oocyte 5S rRNA genes. Molecular and Cellular Biology, 18, 3668–3680.

    PubMed  CAS  Google Scholar 

  28. Guillemette, B., Bataille, A. R., Gevry, N., Adam, M., Blanchette, M., Robert, F., et al. (2005). Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biology, 3, e384.

    PubMed  Google Scholar 

  29. Ramachandran, A., & Schnitzler, G. (2004). Regulating transcription one nucleosome at a time: Nature and function of chromatin remodeling complex products. Recent Research Developments in Molecular and Cellular Biology, 5, 149–170.

    CAS  Google Scholar 

  30. Saha, A., Wittmeyer, J., & Cairns, B. R. (2006). Chromatin remodelling: the industrial revolution of DNA around histones. Nature Reviews. Molecular Cell Biology, 7, 437–447.

    PubMed  CAS  Google Scholar 

  31. Zhang, Z., & Reese, J. C. (2004). Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae. EMBO Journal, 23, 2246–2257.

    PubMed  CAS  Google Scholar 

  32. Parnell, T. J., Huff, J. T., & Cairns, B. R. (2008). RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO Journal, 27, 100–110.

    PubMed  CAS  Google Scholar 

  33. Kim, Y., McLaughlin, N., Lindstrom, K., Tsukiyama, T., & Clark, D. J. (2006). Activation of Saccharomyces cerevisiae HIS3 results in Gcn4p-dependent, SWI/SNF-dependent mobilization of nucleosomes over the entire gene. Molecular and Cellular Biology, 26, 8607–8622.

    PubMed  CAS  Google Scholar 

  34. van Holde, K. E. (1988). Chromatin. In A. Rich (Ed.), Springer series in molecular biology (pp. 289–309). New York: Springer-Verlag.

    Google Scholar 

  35. Ito, T., Bulger, M., Pazin, M. J., Kobayashi, R., & Kadonaga, J. T. (1997). ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell, 90, 145–155.

    PubMed  CAS  Google Scholar 

  36. Varga-Weisz, P. D., Wilm, M., Bonte, E., Dumas, K., Mann, M., & Becker, P. B. (1997). Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature, 388, 598–602.

    PubMed  CAS  Google Scholar 

  37. Lusser, A., Urwin, D. L., & Kadonaga, J. T. (2005). Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nature Structural and Molecular Biology, 12, 160–166.

    PubMed  CAS  Google Scholar 

  38. MacCallum, D. E., Losada, A., Kobayashi, R., & Hirano, T. (2002). ISWI remodeling complexes in Xenopus egg extracts: Identification as major chromosomal components that are regulated by INCENP-aurora B. Molecular Biology of the Cell, 13, 25–39.

    PubMed  CAS  Google Scholar 

  39. Tsukiyama, T., Palmer, J., Landel, C. C., Shiloach, J., & Wu, C. (1999). Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes and Development, 13, 686–697.

    PubMed  CAS  Google Scholar 

  40. Tsukiyama, T., Daniel, C., Tamkun, J., & Wu, C. (1995). ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell, 83, 1021–1026.

    PubMed  CAS  Google Scholar 

  41. Schnitzler, G. R., Cheung, C. L., Hafner, J. H., Saurin, A. J., Kingston, R. E., & Lieber, C. M. (2001). Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Molecular and Cellular Biology, 21, 8504–8511.

    PubMed  CAS  Google Scholar 

  42. Guyon, J. R., Narlikar, G. J., Sullivan, E. K., & Kingston, R. E. (2001). Stability of a human SWI-SNF remodeled nucleosomal array. Molecular and Cellular Biology, 21, 1132–1144.

    PubMed  CAS  Google Scholar 

  43. Yang, J. G., Madrid, T. S., Sevastopoulos, E., & Narlikar, G. J. (2006). The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nature Structural and Molecular Biology, 13, 1078–1083.

    PubMed  CAS  Google Scholar 

  44. He, X., Fan, H. Y., Narlikar, G. J., & Kingston, R. E. (2006). Human ACF1 alters the remodeling strategy of SNF2 h. Journal of Biological Chemistry, 281, 28636–28647.

    PubMed  CAS  Google Scholar 

  45. Zofall, M., Persinger, J., & Bartholomew, B. (2004). Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2. Molecular and Cellular Biology, 24, 10047–10057.

    PubMed  CAS  Google Scholar 

  46. Kagalwala, M. N., Glaus, B. J., Dang, W., Zofall, M., & Bartholomew, B. (2004). Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO Journal, 23, 2092–2104.

    PubMed  CAS  Google Scholar 

  47. Dang, W., Kagalwala, M. N., & Bartholomew, B. (2006). Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Molecular and Cellular Biology, 26, 7388–7396.

    PubMed  CAS  Google Scholar 

  48. Gangaraju, V. K., & Bartholomew, B. (2007). Dependency of ISW1a Chromatin Remodeling on Extranucleosomal DNA. Molecular and Cellular Biology, 27, 3217–3225.

    PubMed  CAS  Google Scholar 

  49. Fazzio, T. G., & Tsukiyama, T. (2003). Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Molecular Cell, 12, 1333–1340.

    PubMed  CAS  Google Scholar 

  50. Whitehouse, I., Rando, O. J., Delrow, J., & Tsukiyama, T. (2007). Chromatin remodelling at promoters suppresses antisense transcription. Nature, 450, 1031–1035.

    PubMed  CAS  Google Scholar 

  51. Whitehouse, I., & Tsukiyama, T. (2006). Antagonistic forces that position nucleosomes in vivo. Nature Structural and Molecular Biology, 13, 633–640.

    PubMed  CAS  Google Scholar 

  52. Maier, V. K., Chioda, M., Rhodes, D., & Becker, P. B. (2008). ACF catalyses chromatosome movements in chromatin fibres. EMBO Journal, 27, 817–826.

    PubMed  CAS  Google Scholar 

  53. Schwarz, P. M., & Hansen, J. C. (1994). Formation and stability of higher order chromatin structures. Contributions of the histone octamer. Journal of Biological Chemistry, 269, 16284–16289.

    PubMed  CAS  Google Scholar 

  54. Dorigo, B., Schalch, T., Kulangara, A., Duda, S., Schroeder, R. R., & Richmond, T. J. (2004). Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science, 306, 1571–1573.

    PubMed  CAS  Google Scholar 

  55. Robinson, P. J., Fairall, L., Huynh, V. A., & Rhodes, D. (2006). EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure. Proceedings of the National Academy of Sciences of the United States of America, 103, 6506–6511.

    PubMed  CAS  Google Scholar 

  56. Carruthers, L. M., Bednar, J., Woodcock, C. L., & Hansen, J. C. (1998). Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding. Biochemistry, 37, 14776–14787.

    PubMed  CAS  Google Scholar 

  57. Woodcock, C. L. (2006). Chromatin architecture. Current Opinion in Structural Biology, 16, 213–220.

    PubMed  CAS  Google Scholar 

  58. Hansen, J. C., & Wolffe, A. P. (1994). A role for histones H2A/H2B in chromatin folding and transcriptional repression. Proceedings of the National Academy of Sciences of the United States of America, 91, 2339–2343.

    PubMed  CAS  Google Scholar 

  59. Francis, N. J., Kingston, R. E., & Woodcock, C. L. (2004). Chromatin compaction by a polycomb group protein complex. Science, 306, 1574–1577.

    PubMed  CAS  Google Scholar 

  60. Shogren-Knaak, M., Ishii, H., Sun, J. M., Pazin, M. J., Davie, J. R., & Peterson, C. L. (2006). Histone H4–K16 acetylation controls chromatin structure and protein interactions. Science, 311, 844–847.

    PubMed  CAS  Google Scholar 

  61. Hansen, J. C., & Lohr, D. (1993). Assembly and structural properties of subsaturated chromatin arrays. Journal of Biological Chemistry, 268, 5840–5848.

    PubMed  CAS  Google Scholar 

  62. Deuring, R., Fanti, L., Armstrong, J. A., Sarte, M., Papoulas, O., Prestel, M., et al. (2000). The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Molecular Cell, 5, 355–365.

    PubMed  CAS  Google Scholar 

  63. Fyodorov, D. V., Blower, M. D., Karpen, G. H., & Kadonaga, J. T. (2004). Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes and Development, 18, 170–183.

    PubMed  CAS  Google Scholar 

  64. Corona, D. F., Siriaco, G., Armstrong, J. A., Snarskaya, N., McClymont, S. A., Scott, M. P., et al. (2007). ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo. PLoS Biology, 5, e232.

    PubMed  Google Scholar 

  65. Lee, K., Kang, M. J., Kwon, S. J., Kwon, Y. K., Kim, K. W., Lim, J. H., et al. (2007). Expansion of chromosome territories with chromatin decompaction in BAF53-depleted interphase cells. Molecular Biology of the Cell, 18, 4013–4023.

    PubMed  CAS  Google Scholar 

  66. Jaskelioff, M., Gavin, I. M., Peterson, C. L., & Logie, C. (2000). SWI-SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state. Molecular and Cellular Biology, 20, 3058–3068.

    PubMed  CAS  Google Scholar 

  67. Lorch, Y., Zhang, M., & Kornberg, R. D. (2001). RSC Unravels the Nucleosome. Molecular Cell, 7, 89–95.

    PubMed  CAS  Google Scholar 

  68. Ramachandran, A., Omar, M., Cheslock, P., & Schnitzler, G. R. (2003). Linker histone H1 modulates nucleosome remodeling by human SWI/SNF. Journal of Biological Chemistry, 278, 48590–48601.

    PubMed  CAS  Google Scholar 

  69. Aoyagi, S., & Hayes, J. J. (2002). hSWI/SNF-catalyzed nucleosome sliding does not occur solely via a twist-diffusion mechanism. Molecular and Cellular Biology, 22, 7484–7490.

    PubMed  CAS  Google Scholar 

  70. Flaus, A., & Owen-Hughes, T. (2003). Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Molecular and Cellular Biology, 23, 7767–7779.

    PubMed  CAS  Google Scholar 

  71. Kassabov, S. R., Zhang, B., Persinger, J., & Bartholomew, B. (2003). SWI/SNF unwraps, slides, and rewraps the nucleosome. Molecular Cell, 11, 391–403.

    PubMed  CAS  Google Scholar 

  72. Saha, A., Wittmeyer, J., & Cairns, B. R. (2005). Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nature Structural and Molecular Biology, 12, 747–755.

    PubMed  CAS  Google Scholar 

  73. Hamiche, A., Sandaltzopoulos, R., Gdula, D. A., & Wu, C. (1999). ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell, 97, 833–842.

    PubMed  CAS  Google Scholar 

  74. Kang, J. G., Hamiche, A., & Wu, C. (2002). GAL4 directs nucleosome sliding induced by NURF. EMBO Journal, 21, 1406–1413.

    PubMed  CAS  Google Scholar 

  75. Stockdale, C., Flaus, A., Ferreira, H., & Owen-Hughes, T. (2006). Analysis of nucleosome repositioning by yeast ISWI and CHD1 chromatin remodeling complexes. Journal of Biological Chemistry, 281, 16279–16288.

    PubMed  CAS  Google Scholar 

  76. Guschin, D., Wade, P. A., Kikyo, N., & Wolffe, A. P. (2000). ATP-dependent histone octamer mobilization and histone deacetylation mediated by the Mi–2 chromatin remodeling complex. Biochemistry, 39, 5238–5245.

    PubMed  CAS  Google Scholar 

  77. Aoyagi, S., Wade, P. A., & Hayes, J. J. (2003). Nucleosome sliding catalyzed by the xMi–2 complex does not occur exclusively via a simple twist-diffusion mechanism. Journal of Biological Chemistry, 278, 30562–30568.

    PubMed  CAS  Google Scholar 

  78. Jin, J., Cai, Y., Yao, T., Gottschalk, A. J., Florens, L., Swanson, S. K., et al. (2005). A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. Journal of Biological Chemistry, 280, 41207–41212.

    PubMed  CAS  Google Scholar 

  79. Langst, G., Bonte, E. J., Corona, D. F., & Becker, P. B. (1999). Nucleosome movement by CHRAC and ISWI without disruption or trans- displacement of the histone octamer. Cell, 97, 843–852.

    PubMed  CAS  Google Scholar 

  80. Corona, D. F., Langst, G., Clapier, C. R., Bonte, E. J., Ferrari, S., Tamkun, J. W., et al. (1999). ISWI is an ATP-dependent nucleosome remodeling factor. Molecular Cell, 3, 239–245.

    PubMed  CAS  Google Scholar 

  81. Eberharter, A., Ferrari, S., Langst, G., Straub, T., Imhof, A., Varga-Weisz, P., et al. (2001). Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO Journal, 20, 3781–3788.

    PubMed  CAS  Google Scholar 

  82. Hartlepp, K. F., Fernandez-Tornero, C., Eberharter, A., Grune, T., Muller, C. W., & Becker, P. B. (2005). The histone fold subunits of Drosophila CHRAC facilitate nucleosome sliding through dynamic DNA interactions. Molecular and Cellular Biology, 25, 9886–9896.

    PubMed  CAS  Google Scholar 

  83. Schwanbeck, R., Xiao, H., & Wu, C. (2004). Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. Journal of Biological Chemistry, 279, 39933–39941.

    PubMed  CAS  Google Scholar 

  84. Kassabov, S. R., Henry, N. M., Zofall, M., Tsukiyama, T., & Bartholomew, B. (2002). High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Molecular and Cellular Biology, 22, 7524–7534.

    PubMed  CAS  Google Scholar 

  85. Gutierrez, J., Paredes, R., Cruzat, F., Hill, D. A., van Wijnen, A. J., Lian, J. B., et al. (2007). Chromatin remodeling by SWI/SNF results in nucleosome mobilization to preferential positions in the rat osteocalcin gene promoter. Journal of Biological Chemistry, 282, 9445–9457.

    PubMed  CAS  Google Scholar 

  86. Rippe, K., Schrader, A., Riede, P., Strohner, R., Lehmann, E., & Langst, G. (2007). DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences of the United States of America, 104, 15635–15640.

    PubMed  CAS  Google Scholar 

  87. Sims, H. I., Lane, J. M., Ulyanova, N. P., & Schnitzler, G. R. (2007). Human SWI/SNF drives sequence-directed repositioning of nucleosomes on C-myc promoter DNA minicircles. Biochemistry, 46, 11377–11388.

    PubMed  CAS  Google Scholar 

  88. Ulyanova, N. P., & Schnitzler, G. R. (2005). Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates. Molecular and Cellular Biology, 25, 11156–11170.

    PubMed  CAS  Google Scholar 

  89. Gavin, I., Horn, P. J., & Peterson, C. L. (2001). SWI/SNF chromatin remodeling requires changes in DNA topology. Molecular Cell, 7, 97–104.

    PubMed  CAS  Google Scholar 

  90. Mohrmann, L., & Verrijzer, C. P. (2005). Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochimica et Biophysica Acta, 1681, 59–73.

    PubMed  CAS  Google Scholar 

  91. Simone, C. (2005). SWI/SNF: The crossroads where extracellular signaling pathways meet chromatin. Journal of Cellular Physiology, 207, 309–314.

    Google Scholar 

  92. Chi, T. (2004). A BAF-centred view of the immune system. Nature Reviews. Immunology, 4, 965–977.

    PubMed  CAS  Google Scholar 

  93. Li, J., Langst, G., & Grummt, I. (2006). NoRC-dependent nucleosome positioning silences rRNA genes. EMBO Journal, 25, 5735–5741.

    PubMed  CAS  Google Scholar 

  94. Pazin, J. J., Bhargava, P., Geiduschek, E. P., & Kadonaga, J. T. (1997). Nucleosome mobility and the maintenance of nucleosome positioning. Science, 276, 809–812.

    PubMed  CAS  Google Scholar 

  95. Angelov, D., Verdel, A., An, W., Bondarenko, V., Hans, F., Doyen, C. M., et al. (2004). SWI/SNF remodeling and p300-dependent transcription of histone variant H2ABbd nucleosomal arrays. EMBO Journal, 23, 3815–3824.

    PubMed  CAS  Google Scholar 

  96. Li, B., Pattenden, S. G., Lee, D., Gutierrez, J., Chen, J., Seidel, C., et al. (2005). Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proceedings of the National Academy of Sciences of the United States of America, 102, 18385–18390.

    PubMed  CAS  Google Scholar 

  97. Doyen, C. M., An, W., Angelov, D., Bondarenko, V., Mietton, F., Studitsky, V. M., et al. (2006). Mechanism of polymerase II transcription repression by the histone variant macroH2A. Molecular and Cellular Biology, 26, 1156–1164.

    PubMed  CAS  Google Scholar 

  98. Ferreira, H., Flaus, A., & Owen-Hughes, T. (2007). Histone modifications influence the Action of Snf2 family remodelling enzymes by different mechanisms. Journal of Molecular Biology, 374, 563–579.

    PubMed  CAS  Google Scholar 

  99. Kundu, S., Horn, P. J., & Peterson, C. L. (2007). SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes and Development, 21, 997–1004.

    PubMed  CAS  Google Scholar 

  100. Horn, P. J., Carruthers, L. M., Logie, C., Hill, D. A., Solomon, M. J., Wade, P. A., et al. (2002). Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nature Structural Biology, 9, 263–267.

    PubMed  CAS  Google Scholar 

  101. Reinke, H., & Horz, W. (2003). Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Molecular Cell, 11, 1599–1607.

    PubMed  CAS  Google Scholar 

  102. Boeger, H., Griesenbeck, J., Strattan, J. S., & Kornberg, R. D. (2003). Nucleosomes unfold completely at a transcriptionally active promoter. Molecular Cell, 11, 1587–1598.

    PubMed  CAS  Google Scholar 

  103. Boeger, H., Griesenbeck, J., Strattan, J. S., & Kornberg, R. D. (2004). Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Molecular Cell, 14, 667–673.

    PubMed  CAS  Google Scholar 

  104. Chen, X., Wang, J., Woltring, D., Gerondakis, S., & Shannon, M. F. (2005). Histone dynamics on the interleukin–2 gene in response to T-cell activation. Molecular and Cellular Biology, 25, 3209–3219

    Google Scholar 

  105. Coisy, M., Roure, V., Ribot, M., Philips, A., Muchardt, C., Blanchard, J. M., et al. (2004). Cyclin A repression in quiescent cells is associated with chromatin remodeling of its promoter and requires brahma/SNF2alpha. Molecular Cell, 15, 43–56.

    PubMed  CAS  Google Scholar 

  106. Lemasson, I., Polakowski, N. J., Laybourn, P. J., & Nyborg, J. K. (2006). Tax-dependent displacement of nucleosomes during transcriptional activation of human T-cell leukemia virus, type 1. Journal of Biological Chemistry, 281, 13075–13083.

    PubMed  CAS  Google Scholar 

  107. Liu, H., Mulholland, N., Fu, H., & Zhao, K. (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Molecular and Cellular Biology, 26, 2550–2559.

    PubMed  CAS  Google Scholar 

  108. Erkina, T. Y., & Erkine, A. M. (2006). Displacement of histones at promoters of Saccharomyces cerevisiae heat shock genes is differentially associated with histone H3 acetylation. Molecular and Cellular Biology, 26, 7587–7600.

    PubMed  CAS  Google Scholar 

  109. Erkina, T. Y., Tschetter, P. A., & Erkine, A. M. (2008). Different requirements of the SWI/SNF complex for robust nucleosome displacement at promoters of heat shock factor and Msn2- and Msn4-regulated heat shock genes. Molecular and Cellular Biology, 28, 1207–1217.

    PubMed  CAS  Google Scholar 

  110. Schermer, UJK, P Horz, W (2005). Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Molecular Cell, 19, 279–285.

  111. Adkins, M. W., Williams, S. K., Linger, J., & Tyler, J. K. (2007). Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Molecular and Cellular Biology, 27, 6372–6382.

    PubMed  CAS  Google Scholar 

  112. Barbaric, S., Luckenbach, T., Schmid, A., Blaschke, D., Horz, W., & Korber, P. (2007). Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. Journal of Biological Chemistry, 282, 27610–27621.

    PubMed  CAS  Google Scholar 

  113. Schwabish, M. A., & Struhl, K. (2007). The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Molecular and Cellular Biology, 27, 6987–6995.

    PubMed  CAS  Google Scholar 

  114. Korber, P., Barbaric, S., Luckenbach, T., Schmid, A., Schermer, U. J., Blaschke D., & Horz, W. (2006). The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. Journal of Biological Chemistry, 281, 5539–5545.

    Google Scholar 

  115. Adkins, M. W., Howar, S. R., & Tyler, J. K. (2004). Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Molecular Cell, 14, 657–666.

    PubMed  CAS  Google Scholar 

  116. Workman, J. L. (2006). Nucleosome displacement in transcription. Genes and Development, 20, 2009–2017.

    PubMed  CAS  Google Scholar 

  117. Phelan, M. L., Schnitzler, G. R., & Kingston, R. E. (2000). Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases. Molecular and Cellular Biology, 20, 6380–6389.

    PubMed  CAS  Google Scholar 

  118. Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Molecular Cell, 12, 1599–1606.

    PubMed  CAS  Google Scholar 

  119. Lorch, Y., Zhang, M., & Kornberg, R. D. (1999). Histone octamer transfer by a chromatin-remodeling complex. Cell, 96, 389–392.

    PubMed  CAS  Google Scholar 

  120. Lorch, Y., Maier-Davis, B., & Kornberg, R. D. (2006). Chromatin remodeling by nucleosome disassembly in vitro. Proceedings of the National Academy of Sciences of the United States of America, 103, 3090–3093.

    PubMed  CAS  Google Scholar 

  121. Chandy, M., Gutierrez, J. L., Prochasson, P., & Workman, J. L. (2006). SWI/SNF displaces SAGA-acetylated nucleosomes. Eukaryotic Cell, 5, 1738–1747.

    PubMed  CAS  Google Scholar 

  122. Gutierrez, J. L., Chandy, M., Carrozza, M. J., & Workman, J. L. (2007). Activation domains drive nucleosome eviction by SWI/SNF. EMBO Journal, 26, 730–740.

    PubMed  CAS  Google Scholar 

  123. Vicent, G. P., Nacht, A. S., Smith, C. L., Peterson, C. L., Dimitrov, S., & Beato, M. (2004). DNA instructed displacement of histones H2A and H2B at an inducible promoter. Molecular Cell, 16, 439–452.

    PubMed  CAS  Google Scholar 

  124. Fleming, A. B., & Pennings, S. (2007). Tup1-Ssn6 and Swi-Snf remodelling activities influence long-range chromatin organization upstream of the yeast SUC2 gene. Nucleic Acids Research, 35, 5520–5531.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Tufts University School of Medicine, 136 Harrison, Ave., Boston, MA, 02111, USA

    Gavin R. Schnitzler

Authors
  1. Gavin R. Schnitzler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gavin R. Schnitzler.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schnitzler, G.R. Control of Nucleosome Positions by DNA Sequence and Remodeling Machines. Cell Biochem Biophys 51, 67–80 (2008). https://doi.org/10.1007/s12013-008-9015-6

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12013-008-9015-6

Keywords

Search

Navigation