ArticleNucleic acids research2004
A determining influence for CpG dinucleotides on nucleosome positioning in vitro.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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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
25 citing papers in PubMed, 60 citations in OpenAlex.
- Splicing deficiency is driven by genomic erosion in non-recombining algal mating-type chromosomes.PLoS biology · 2026Article
- Extensive splicing deficiency in a degenerating mating-type chromosome.bioRxiv : the preprint server for biology · 2025Article
- Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes.Genome biology and evolution · 2017Review
- The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni.PLoS neglected tropical diseases · 2017Article
- The effects of cytosine methylation on general transcription factors.Scientific reports · 2016Article
- Dynamics of nucleosome assembly and effects of DNA methylation.The Journal of biological chemistry · 2015Article
- DNA methylation effects on tetra-nucleosome compaction and aggregation.Biophysical journal · 2014Article
- Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.BMC bioinformatics · 2014Article
- Making the bend: DNA tertiary structure and protein-DNA interactions.International journal of molecular sciences · 2014Review
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.The journal of physical chemistry. B · 2013Article
- DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes.Oncogene · 2013Article
- DNA methylation regulated nucleosome dynamics.Scientific reports · 2013Article
- Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.PLoS computational biology · 2013Article
- The effect of DNA CpG methylation on the dynamic conformation of a nucleosome.Biophysical journal · 2012Article
- Impact of methylation on the physical properties of DNA.Biophysical journal · 2012Article
- Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.PLoS genetics · 2011Article
- Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize.BMC plant biology · 2010Article
- Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro.Journal of biomolecular structure & dynamics · 2010Article
- Repertoires of the nucleosome-positioning dinucleotides.PloS one · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA sequence information that directs the translational positioning of nucleosomes can be attenuated by cytosine methylation when a short run of CpG dinucleotides is located close to the dyad axis of the nucleosome. Here, we show that point mutations introduced to re-pattern methylation at the (CpG)3 element in the chicken betaA-globin promoter sequence themselves strongly influenced nucleosome formation in reconstituted chromatin. The disruptive effect of cytosine methylation on nucleosome formation was found to be determined by the sequence context of CpG dinucleotides, not just their location in the positioning sequence. Additional mutations indicated that methylation can also promote the occupation of certain nucleosome positions. DNase I analysis demonstrated that these genetic and epigenetic modifications altered the structural characteristics of the (CpG)3 element. Our findings support a proposal that the intrinsic structural properties of the DNA at the -1.5 site, as occupied by (CpG)3 in the nucleosome studied, can be decisive for nucleosome formation and stability, and that changes in anisotropic DNA bending or flexibility at this site explain why nucleosome positioning can be exquisitely sensitive to genetic and epigenetic modification of the DNA sequence.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.