The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
Nucleosome positioning signals in genomic DNA
Open accessAbstract
Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae whose nucleosome binding affinities have been experimentally determined (Yuan et al. 2005) to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of S. cerevisiae and identified strong periodicity within 199 center-aligned mononucleosomes studied recently (Segal et al. 2006) despite there being no periodicity information used to train the support vector machine. Our analysis suggests that only a subset of nucleosomes are likely to be positioned by intrinsic sequence signals. This observation is consistent with the available experimental data and is inconsistent with the proposal of a nucleosome positioning code. Finally, we show that intrinsic nucleosome positioning signals are both more inhibitory and more variable in promoter regions than in open reading frames in S. cerevisiae.
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Chromatin structure analyses identify miRNA promoters
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Mechanisms that Specify Promoter Nucleosome Location and Identity
Hartley, P. D., & Madhani, H. D. (2009) · Cell · doi:10.1016/j.cell.2009.02.043 · Cited by 406
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Mirny, L. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913805107 · Cited by 349
Tolstorukov, M. Y., Sansam, C. G., Lu, P., Koellhoffer, E. C., Helming, K. C., Alver, B. H., Tillman, E. J., Evans, J. A., Wilson, B. G., Park, P. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302209110 · Cited by 190
Metadata
- Authors
- Peckham, H. E., Thurman, R. E., Fu, Y., Stamatoyannopoulos, J. A., Noble, W. S., Struhl, K., & Weng, Z.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-07-09
- Volume
- 17
- Issue
- 8
- Pages
- 1170-1177
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2134314200
- Cited by
- 316
- References
- 64
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Peckham, H. E., Thurman, R. E., Fu, Y., Stamatoyannopoulos, J. A., Noble, W. S., Struhl, K., & Weng, Z. (2007). Nucleosome positioning signals in genomic DNA. Genome Research. https://doi.org/10.1101/gr.6101007
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