ArticlePLoS computational biology2008
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 281 papers, 2 of them syntheses that pooled it.
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.
The trial behind it
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
281 citing papers in PubMed, 2 syntheses or guidelines pooled it, 476 citations in OpenAlex.
- Pooled it
- Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules.BMC genomics · 2013Pooled it
- Cis and trans acting factors involved in human cytomegalovirus experimental and natural latent infection of CD14 (+) monocytes and CD34 (+) cells.PLoS pathogens · 2013Trial
- Article
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- Environmental impacts on gene expression noise and its relationship with fitness.bioRxiv : the preprint server for biology · 2026Article
- Sus1 Modulates Chromatin Remodeling and Gene Expression via the Cell Wall Integrity Pathway in Saccharomyces cerevisiae.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- The basic domain of Suv39h2 buffers mitoxantrone-induced heterochromatin destabilization.iScience · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences.DNA repair · 2025Article
- Short tandem repeats delineate gene bodies across eukaryotes.Nature communications · 2024Article
- How genotype-by-environment interactions on fitness emerge.Nature ecology & evolution · 2024Article
- Comparison of Nucleosome Landscapes Between Porcine Embryonic Fibroblasts and GV Oocytes.Animals : an open access journal from MDPI · 2024Article
- Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data.Genomics, proteomics & bioinformatics · 2024Review
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery.Nucleic acids research · 2024Article
- Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes.Nucleus (Austin, Tex.) · 2023Review
- Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects.International journal of molecular sciences · 2023Article
- Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy.Science advances · 2023Article
221 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of approximately 380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition.
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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.