Skip to main content Accessibility help
×
Home
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 2
  • Print publication year: 2012
  • Online publication date: August 2012

4 - Nucleosome positioningin promoters:

from Part I - Basics of chromatin biology and biochemistry

References

Balasubramanian, S., Xu, F., and Olson, W. K. (2009). DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophysics Journal, 96, 2245–2260.
Bresnick, E. H., John, S., and Hager, G. L. (1991). Histone hyperacetylation does not alter the positioning or stability of phased nucleosomes on the mouse mammary tumor virus long terminal repeat. Biochemistry, 30, 3490–3497.
Brukner, I., Jurukovski, V., and Savic, A. (1990). Sequence-dependent structural variations of DNA revealed by DNase I. Nucleic Acids Research, 18, 891–894.
Brukner, I., Sanchez, R., Suck, D., and Pongor, S. (1995). Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO Journal, 14, 1812–1818.
Cao, H., Widlund, H. R., Simonsson, T., and Kubista, M. (1998). TGGA repeats impair nucleosome formation. Journal of Molecular Biology, 281, 253–260.
Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., et al. (2010). Relationship between nucleosome positioning and DNA methylation. Nature, 466, 388–392.
Davey, C. S., Pennings, S., Reilly, C., Meehan, R. R., and Allan, J. (2004). A determining influence for CpG dinucleotides on nucleosome positioning in vitro. Nucleic Acids Research, 32, 4322–4331.
Dechassa, M. L., Sabri, A., Pondugula, S., et al. (2010). SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Molecular Cell, 38, 590–602.
Delcourt, S. G. and Blake, R. D. (1991). Stacking energies in DNA. Journal of Biological Chemistry, 266, 15 160–15 169.
Dennis, J. H., Fan, H. Y., Reynolds, S. M., et al. (2007). Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research, 17, 928–939.
Gabrielian, A. and Pongor, S. (1996). Correlation of intrinsic DNA curvature with DNA property periodicity. FEBS Letters, 393, 65–68.
Godde, J. S. and Wolffe, A. P. (1996). Nucleosome assembly on CTG triplet repeats. Journal of Biological Chemistry, 271, 15 222–15 229.
Godde, J. S., Kass, S. U., Hirst, M. C., and Wolffe, A. P. (1996). Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. Journal of Biological Chemistry, 271, 24 325–24 328.
Goodsell, D. S. and Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucleic Acids Research, 22, 5497–5503.
Gupta, S., Dennis, J., Thurman, R. E., et al. (2008). Predicting human nucleosome occupancy from primary sequence. PLoS Computational Biology, 4, e1000134.
Guttman, M., Amit, I., Garber, M., et al. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223–227.
Hayes, J. J., Clark, D. J., and Wolffe, A. P. (1991). Histone contributions to the structure of DNA in the nucleosome. Proceedings of the National Academy of Sciences USA, 88, 6829–6833.
He, H. H., Meyer, C. A., Shin, H., et al. (2010). Nucleosome dynamics define transcriptional enhancers. Nature Genetics, 42, 343–347.
Hodges, C., Bintu, L., Lubkowska, L., Kashlev, M., and Bustamante, C. (2009). Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science, 325, 626–628.
Hogan, M. E., Rooney, T. F., and Austin, R. H. (1987). Evidence for kinks in DNA folding in the nucleosome. Nature, 328, 554–557.
Horz, W. and Altenburger, W. (1981). Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Research, 9, 2643–2658.
Hu, J. L., Zhou, B. O., Zhang, R. R., et al. (2009). The N-terminus of histone H3 is required for de novo DNA methylation in chromatin. Proceedings of the National Academy of Sciences USA, 106, 22187–22192.
Huarte, M., Guttman, M., Feldser, D., et al. (2010). A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142, 409–419.
Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., and Trifonov, E. N. (1996). Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. Journal of Molecular Biology, 262, 129–139.
Jackson, J. R. and Benyajati, C. (1993). DNA-histone interactions are sufficient to position a single nucleosome juxtaposing Drosophila Adh adult enhancer and distal promoter. Nucleic Acids Research, 21, 957–967.
Jin, C., Zang, C., Wei, G., et al. (2009). H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions. Nature Genetics, 41, 941–945.
Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., et al. (2009). The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362–366.
Keenen, B., Qi, H., Saladi, S. V., Yeung, M., and de la Serna, I. L. (2010). Heterogeneous SWI/SNF chromatin remodeling complexes promote expression of microphthalmia-associated transcription factor target genes in melanoma. Oncogene, 29, 81–92.
Khalil, A. M., Guttman, M., Huarte, M., et al. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences USA, 106, 11 667–11 672.
Kulaeva, O. I., Gaykalova, D. A., Pestov, N. A., et al. (2009). Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nature Structural and Molecular Biology, 16, 1272–1278.
Lahm, A. and Suck, D. (1991). DNase I-induced DNA conformation. II. A structure of a DNase I-octamer complex. Journal of Molecular Biology, 222, 645–667.
Lantermann, A., Stralfors, A., Fagerstrom-Billai, F., Korber, P., and Ekwall, K. (2009). Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods, 48, 218–225.
Lantermann, A. B., Straub, T., Stralfors, A., et al. (2010). Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nature Structural and Molecular Biology, 17, 251–257.
Lee, W., Tillo, D., Bray, N., et al. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics, 39, 1235–1244.
Levitsky, V. G. (2004). RECON: a program for prediction of nucleosome formation potential. Nucleic Acids Research, 32, W346–349.
Lowary, P. T., and Widom, J. (1997). Nucleosome packaging and nucleosome positioning of genomic DNA. Proceedings of the National Academy of Sciences USA, 94, 1183–1188.
Lowary, P. T. and Widom, J. (1998). New DNA sequence rules for high-affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology, 276, 19–42.
Luger, K. and Richmond, T. J. (1998). DNA binding within the nucleosome core. Current Opinion in Structural Biology, 8, 33–40.
Lupien, M., Eeckhoute, J., Meyer, C. A., et al. (2008). FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell, 132, 958–970.
Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., et al. (2008). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research, 18, 1073–1083.
Mirzabekov, A. D. and Rich, A. (1979). Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. Proceedings of the National Academy of Sciences USA, 76, 1118–1121.
Ozsolak, F., Song, J. S., Liu, X. S., and Fisher, D. E. (2007). High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology, 25, 244–248.
Ozsolak, F., Poling, L. L., Wang, Z., et al. (2008). Chromatin structure analyses identify miRNA promoters. Genes & Development, 22, 3172–3183.
Peckham, H. E., Thurman, R. E., Fu, Y., et al. (2007). Nucleosome positioning signals in genomic DNA. Genome Research, 17, 1170–1177.
Reynolds, S., Bilmes, J., and Noble, W. (2009a). Low frequency oscillations in single-nucleotide content play a role in nucleosome positioning in H. sapiens. In Proceedings of the 13th International Conference on Research in Computational Molecular Biology (RECOMB).
Reynolds, S., Bilmes, J., and Noble, W. (2009b). On the relationship between DNA periodicity and local chromatin structure. In Proceedings of the 13th International Conference on Research in Computational Molecular Biology (RECOMB).
Reynolds, S., Bilmes, J., and Noble, W. (2010). Predicting nucleosome positioning using multiple evidence tracks. In Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB).
Robinson, P. J. and Rhodes, D. (2006). Structure of the ‘30 nm’ chromatin fibre: a key role for the linker histone. Current Opinion in Structural Biology, 16, 336–343.
Routh, A., Sandin, S., and Rhodes, D. (2008). Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proceedings of the National Academy of Sciences USA, 105, 8872–8877.
Satchwell, S. C., Drew, H. R., and Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology, 191, 659–675.
Schones, D. E., Cui, K., Cuddapah, S., et al. (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell, 132, 887–898.
Segal, E. and Widom, J. (2009). Poly(dA:dT) tracts: major determinants of nucleosome organization. Current Opinion in Structural Biology, 19, 65–71.
Segal, E., Fondufe-Mittendorf, Y., Chen, L., et al. (2006). A genomic code for nucleosome positioning. Nature, 442, 772–778.
Segal, M. R. (2008). Re-cracking the nucleosome positioning code. Statistical Applications in Genetics and Molecular Biology, 7, Article14.
Suck, D. (1994). DNA recognition by DNase I. Journal of Molecular Recognition, 7, 65–70.
Thomas, G. H. and Elgin, S. C. (1988). Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO Journal, 7, 2191–2201.
Weston, S. A., Lahm, A., and Suck, D. (1992). X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 Å resolution. Journal of Molecular Biology, 226, 1237–1256.
Wyrick, J. J., Holstege, F. C., Jennings, E. G., et al. (1999). Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature, 402, 418–421.
Yuan, G. C. and Liu, J. S. (2008). Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology, 4, e13.
Yuan, G. C., Liu, Y. J., Dion, M. F., et al. (2005). Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626–630.
Zhang, Y., Moqtaderi, Z., Rattner, B. P., et al. (2009). Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nature Structural and Molecular Biology, 16, 847–852.
Zhou, Y., Schmitz, K. M., Mayer, C., et al. (2009). Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing. Nature Cell Biology, 11, 1010–1016.
Zofall, M., Persinger, J., Kassabov, S. R., and Bartholomew, B. (2006). Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nature Structural and Molecular Biology, 13, 339–346.