The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome
Open accessAbstract
Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by deep-sequencing and high-density tiling arrays, and we discovered an array of well-positioned nucleosomes flanking sites occupied by the insulator binding protein CTCF across the human genome. These nucleosomes are highly enriched for the histone variant H2A.Z and 11 histone modifications. The distances between the center positions of the neighboring nucleosomes are largely invariant, and we estimate them to be 185 bp on average. Surprisingly, subsets of nucleosomes that are enriched in different histone modifications vary greatly in the lengths of DNA protected from micrococcal nuclease cleavage (106-164 bp). The nucleosomes enriched in those histone modifications previously implicated to be correlated with active transcription tend to contain less protected DNA, indicating that these modifications are correlated with greater DNA accessibility. Another striking result obtained from our analysis is that nucleosomes flanking CTCF sites are much better positioned than those downstream of transcription start sites, the only genomic feature previously known to position nucleosomes genome-wide. This nucleosome-positioning phenomenon is not observed for other transcriptional factors for which we had genome-wide binding data. We suggest that binding of CTCF provides an anchor point for positioning nucleosomes, and chromatin remodeling is an important component of CTCF function.
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Cites
High-Resolution Profiling of Histone Methylations in the Human Genome
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“H3K4me1, H4K20me1, and to some extent H3K9me2 [16,36]) correspond to the least protection against MNase, suggesting that increasing accessibility of the ends of nucleosomal DNA may be a mechanism for transcriptional activation.”
BackgroundInfluentialSelf-citationA Global Map of p53 Transcription-Factor Binding Sites in the Human Genome
Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., et al. (2006) · Cell · doi:10.1016/j.cell.2005.10.043 · Cited by 1,141
Self-citationEvidence for nucleosome depletion at active regulatory regions genome-wide
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CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
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Dynamics of Replication-Independent Histone Turnover in Budding Yeast
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CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus
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Cited by
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The Human Transcription Factors
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Organizational principles of 3D genome architecture
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Histones: annotating chromatin
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Chromatin Domains: The Unit of Chromosome Organization
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Metadata
- Authors
- Fu, Y., Sinha, M., Peterson, C. L., & Weng, Z.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-07-25
- Volume
- 4
- Issue
- 7
- Pages
- e1000138
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2086038224
- Cited by
- 394
- References
- 10
- FWCI
- 11.42
- Type
- journal article
- Language
- en
- Open access
- gold
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