ArticleGenome research2014
The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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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Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Review
- Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells.Nature communications · 2021Article
- Chromatin dynamics: Nucleosome occupancy and sensitivity as determinants of gene expression and cell fate.Journal of cancer biology · 2021Article
- MNase Profiling of Promoter Chromatin inG3 (Bethesda, Md.) · 2020Article
- Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters.Nature communications · 2020Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- iSeg: an efficient algorithm for segmentation of genomic and epigenomic data.BMC bioinformatics · 2018Article
- The coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity.Nucleus (Austin, Tex.) · 2017Review
- The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler.Journal of molecular biology · 2017Article
- Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.Genes & development · 2017Article
- Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome.BioEssays : news and reviews in molecular, cellular and developmental biology · 2017Review
- Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Categorical spectral analysis of periodicity in nucleosomal DNA.Nucleic acids research · 2016Article
- Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response.Oncotarget · 2016Article
- Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis.Virologica Sinica · 2015Review
- Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy.Genomics data · 2015Article
- Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes.PloS one · 2015Article
- DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.PloS one · 2015Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
Abstract
Nucleosome occupancy plays a key role in regulating access to eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 h post-KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro-assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 h post-KSHV reactivation. We suggest a model in which loci are held in an unfavorable chromatin architecture and "spring" to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.
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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.