ArticleMolecular and cellular biology2012
Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner.
Article in Molecular and cellular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 88 citations in OpenAlex.
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
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- The nucleosome remodeling and deacetylase-SWItch/sucrose non-fermentable antagonism regulates the coordinated activation of epithelial-to-mesenchymal transition and inflammation in oral cancer.Journal of the National Cancer Institute · 2025Article
- Functional Role of Bap170 Domains in Enhancer-Dependent Gene Activity in Drosophila melanogaster.Doklady. Biochemistry and biophysics · 2025Article
- Epigenetic dysregulation in pancreatic cancer: emerging biomarkers and clinical applications.Frontiers in epigenetics and epigenomics · 2025Review
- TheInternational journal of molecular sciences · 2024Article
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- Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression.Doklady. Biochemistry and biophysics · 2024Article
- In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin.eLife · 2021Article
- Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription inInternational journal of molecular sciences · 2021Article
- Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability.International journal of molecular sciences · 2020Review
- Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.International journal of molecular sciences · 2020Article
- Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer.Genes & development · 2019Review
- Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.Nucleic acids research · 2019Article
- The CHD6 chromatin remodeler is an oxidative DNA damage response factor.Nature communications · 2019Article
- The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.Molecular cell · 2018Article
- CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality.Nucleic acids research · 2017Article
- Covalent Modifications of Histone H3K9 Promote Binding of CHD3.Cell reports · 2017Article
- EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes.Nature communications · 2017Article
- Human INO80/YY1 chromatin remodeling complex transcriptionally regulates the BRCA2- and CDKN1A-interacting protein (BCCIP) in cells.Protein & cell · 2016Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nucleosome is the fundamental repeating unit of eukaryotic chromatin. Here, we assessed the interplay between DNA sequence and ATP-dependent chromatin-remodeling factors (remodelers) in the nucleosomal organization of a eukaryotic genome. We compared the genome-wide distribution of Drosophila NURD, (P)BAP, INO80, and ISWI, representing the four major remodeler families. Each remodeler has a unique set of genomic targets and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two distinct ways. NURD, (P)BAP, and INO80 increase histone density at their target sequences, which intrinsically disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Remodelers influence nucleosome organization genome-wide, reflecting their high genomic density and the propagation of nucleosome redistribution beyond remodeler binding sites. In transcriptionally silent early embryos, nucleosome organization correlates with intrinsic histone-DNA sequence preferences. Following differential expression of the genome, however, this relationship diminishes and eventually disappears. We conclude that the cellular nucleosome landscape is the result of the balance between DNA sequence-driven nucleosome placement and active nucleosome repositioning by remodelers and the transcription machinery.
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