ArticleNucleic acids research2010
Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
- De novo reconstitution of chromatin using wheat germ cell-free protein synthesis.FEBS open bio · 2021Article
- Reconstitution of Drosophila and human chromatins by wheat germ cell-free co-expression system.BMC biotechnology · 2020Article
- Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies.Protein science : a publication of the Protein Society · 2017Review
- Article
- DNA methylation regulated nucleosome dynamics.Scientific reports · 2013Article
- Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Article
- An effect of DNA sequence on nucleosome occupancy and removal.Nature structural & molecular biology · 2011Article
- Sequence-specific ultrasonic cleavage of DNA.Biophysical journal · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several periodic motifs have been implicated in facilitating the bending of DNA around the histone core of the nucleosome. For example, di-nucleotides AA/TT/TA and GC at ∼10-bp periods, but offset by 5 bp, are found with higher-than-expected occurrences in aligned nucleosomal DNAs in vitro and in vivo. Additionally, regularly oscillating period-10 trinucleotide motifs non-T, A/T, G and their complements have been implicated in the formation of regular nucleosome arrays. The effects of these periodic motifs on nucleosome formation have not been systematically tested directly by competitive reconstitution assays. We show that, in general, none of these period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation. The influence of periodic TAs on nucleosome formation is appreciable; with some of the 200-bp DNAs out-competing bulk nucleosomal DNA by more than 400-fold. Only the nucleotides immediately flanking TA influence its nucleosome-forming ability. Period-10 TA, when flanked by a pair of permissive nucleotides, facilitates DNA bending through compression of the minor groove. The free energy change for nucleosome formation decreases linearly with the number of consecutive TAs, up to eight. We suggest how these data can be reconciled with previous findings.
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