The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Open accessAbstract
Most nucleosomes are well-organized at the 5′ ends of S. cerevisiae genes where “−1” and “+1” nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the −1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3′ NFR that is present at >95% of all genes. 3′ NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3′ NFRs in gene looping.
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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
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
Perocchi, F., Xu, Z., Clauder-Münster, S., & Steinmetz, L. M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm683 · Cited by 193
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Chromatin accessibility and the regulatory epigenome
Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793
Mechanisms and Consequences of Alternative Polyadenylation
Di Giammartino, D. C., Nishida, K., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.017 · Cited by 737
Chromatin structure analyses identify miRNA promoters
Ozsolak, F., Poling, L. L., Wang, Z., Liu, H., Liu, X. S., Roeder, R. G., Zhang, X., Song, J. S., & Fisher, D. E. (2008) · Genes & Development · doi:10.1101/gad.1706508 · Cited by 678
Determinants 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
Metadata
- Authors
- Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I., & Pugh, B. F.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-06-12
- Volume
- 18
- Issue
- 7
- Pages
- 1073-1083
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2106448802
- Cited by
- 672
- References
- 2
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I., & Pugh, B. F. (2008). A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research. https://doi.org/10.1101/gr.078261.108
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