ArticleNucleic acids research2010
Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?
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 42 papers.
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Who cites it
42 citing papers in PubMed.
- Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.iScience · 2025Article
- Absolute nucleosome occupancy map for theGenome research · 2019Article
- Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.Plant biotechnology journal · 2019Article
- In silico evidence for sequence-dependent nucleosome sliding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations.Scientific reports · 2016Article
- Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.Nucleic acids research · 2016Article
- Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.Biochemical and biophysical research communications · 2016Article
- Categorical spectral analysis of periodicity in nucleosomal DNA.Nucleic acids research · 2016Article
- Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.PloS one · 2016Article
- A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.PloS one · 2016Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- Canonical nucleosome organization at promoters forms during genome activation.Genome research · 2014Article
- Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity.The open biomedical engineering journal · 2014Article
- A comparison of in vitro nucleosome positioning mapped with chicken, frog and a variety of yeast core histones.Journal of molecular biology · 2013Article
- Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.Journal of molecular biology · 2013Article
- Characterizing and measuring bias in sequence data.Genome biology · 2013Article
- A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription.PLoS genetics · 2013Article
- Effects of DNA methylation on nucleosome stability.Nucleic acids research · 2013Article
- Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.PLoS computational biology · 2013Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Large-scale and genome-wide studies have concluded that approximately 80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo.
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