The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
Open accessAbstract
We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.
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Citations
Cites
Evidence for nucleosome depletion at active regulatory regions genome-wide
Lee, C.-K., Shibata, Y., Rao, B., Strahl, B. D., & Lieb, J. D. (2004) · Nature Genetics · doi:10.1038/ng1400 · Cited by 738
Dynamics of Replication-Independent Histone Turnover in Budding Yeast
Dion, M. F., Kaplan, T., Kim, M., Buratowski, S., Friedman, N., & Rando, O. J. (2007) · Science · doi:10.1126/science.1134053 · Cited by 556
Schwabish, M. A., & Struhl, K. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00717-07 · Cited by 158
Self-citation
Cited by
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
Determinants of nucleosome positioning
Struhl, K., & Segal, E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2506 · Cited by 686
Self-citationDeterminants of nucleosome organization in primary human cells
Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., & Sidow, A. (2011) · Nature · doi:10.1038/nature10002 · Cited by 677
Recombination centres and the orchestration of V(D)J recombination
Schatz, D. G., & Ji, Y. (2011) · Nature Reviews Immunology · doi:10.1038/nri2941 · Cited by 658
Understanding nucleosome dynamics and their links to gene expression and DNA replication
Lai, W. K. M., & Pugh, B. F. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.47 · Cited by 495
Metadata
- Authors
- Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G., Snyder, M., Kadonaga, J. T., Liu, X. S., & Struhl, K.
- Venue
- Nature Structural & Molecular Biology
- Published
- 2009-07-20
- Volume
- 16
- Issue
- 8
- Pages
- 847-852
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2073374533
- Cited by
- 365
- References
- 3
- FWCI
- 21.24
- Type
- journal article
- Language
- en
- Open access
- green
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- Zhang, Y., Moqtaderi, Z., Rattner, B. P., Euskirchen, G., Snyder, M., Kadonaga, J. T., Liu, X. S., & Struhl, K. (2009). Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nature Structural & Molecular Biology. https://doi.org/10.1038/nsmb.1636
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