ArticleNucleic acids research2009
Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 99 citations in OpenAlex.
- Juvenile hormone-mediated chromatin remodelling by cumulative action of downstream transcription factors, Hairy and Krüppel homolog 1.Communications biology · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- An Update on Potential Molecular Biomarkers of Dietary Phytochemicals Targeting Lung Cancer Interception and Prevention.Pharmaceutical research · 2023Review
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
- Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.Epigenetics · 2021Article
- Histone acetylation and the role of histone deacetylases in normal cyclic endometrium.Reproductive biology and endocrinology : RB&E · 2020Review
- Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules.Frontiers in genetics · 2020Article
- The histone modification reader ZCWPW1 is required for meiosis prophase I in male but not in female mice.Science advances · 2019Article
- Tat inhibition by didehydro-Cortistatin A promotes heterochromatin formation at the HIV-1 long terminal repeat.Epigenetics & chromatin · 2019Article
- Epigenetics in amyotrophic lateral sclerosis: a role for histone post-translational modifications in neurodegenerative disease.Translational research : the journal of laboratory and clinical medicine · 2019Review
- A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes.BMC medical genomics · 2018Article
- The Latest Twists in Chromatin Remodeling.Biophysical journal · 2018Review
- Epigenetic regulation of long non-coding RNAs in gastric cancer.Oncotarget · 2018Review
- Critical effects of epigenetic regulation in pulmonary arterial hypertension.Cellular and molecular life sciences : CMLS · 2017Review
- Diabetic retinopathy: reversibility of epigenetic modifications and new therapeutic targets.Cell & bioscience · 2017Review
- Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.Scientific reports · 2016Article
- Nucleosome architecture throughout the cell cycle.Scientific reports · 2016Article
- ARID1B-mediated disorders: Mutations and possible mechanisms.Intractable & rare diseases research · 2015Review
- EpiFactors: a comprehensive database of human epigenetic factors and complexes.Database : the journal of biological databases and curation · 2015Article
- Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders.Frontiers in behavioral neuroscience · 2015Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4(+) T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.
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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.