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The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
- Source :
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PLoS genetics [PLoS Genet] 2008 Jul 25; Vol. 4 (7), pp. e1000138. Date of Electronic Publication: 2008 Jul 25. - Publication Year :
- 2008
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Abstract
- 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.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Binding Sites
CCCTC-Binding Factor
Chromatin Assembly and Disassembly physiology
Histones genetics
Histones metabolism
Humans
Micrococcal Nuclease pharmacology
Transcription Factors metabolism
DNA-Binding Proteins genetics
DNA-Binding Proteins metabolism
Genome, Human
Nucleosomes genetics
Nucleosomes metabolism
Repressor Proteins genetics
Repressor Proteins metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1553-7404
- Volume :
- 4
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- PLoS genetics
- Publication Type :
- Academic Journal
- Accession number :
- 18654629
- Full Text :
- https://doi.org/10.1371/journal.pgen.1000138