ArticleGenome biology2004
Global nucleosome occupancy in yeast.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers.
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Who cites it
189 citing papers in PubMed, 355 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Regulation of Catalase Expression and Activity byJournal of fungi (Basel, Switzerland) · 2024Article
- Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes.Nucleus (Austin, Tex.) · 2023Review
- Structures of transcription preinitiation complex engaged with the +1 nucleosome.Nature structural & molecular biology · 2023Article
- Manipulating chromatin architecture in C. elegans.Epigenetics & chromatin · 2022Article
- Article
- Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq.Stem cell reports · 2022Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Proteasome Activator Blm10 Regulates Transcription Especially During Aging.Current genomics · 2021Article
- H3K4me2 ChIP-Seq reveals the epigenetic landscape during mushroom formation and novel developmental regulators of Schizophyllum commune.Scientific reports · 2021Article
- Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis.PloS one · 2021Article
- The Transcription Factor SomA Synchronously Regulates Biofilm Formation and Cell Wall Homeostasis inmBio · 2020Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
- Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.Nature biotechnology · 2020Article
- Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.Genome research · 2019Article
- A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin.The Journal of biological chemistry · 2018Article
- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- Intrinsic cooperativity potentiates paralleleLife · 2018Article
- LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.Bioinformatics (Oxford, England) · 2018Article
129 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAlthough eukaryotic genomes are generally thought to be entirely chromatin-associated, the activated PHO5 promoter in yeast is largely devoid of nucleosomes. We systematically evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantifying enrichment by microarrays.
resultsNucleosome depletion is observed in promoters that regulate active genes and/or contain multiple evolutionarily conserved motifs that recruit transcription factors. The Rap1 consensus was the only binding motif identified in a completely unbiased search of nucleosome-depleted promoters. Nucleosome depletion in the vicinity of Rap1 consensus sites in ribosomal protein gene promoters was also observed by real-time PCR and micrococcal nuclease digestion. Nucleosome occupancy in these regions was increased by the small molecule rapamycin or, in the case of the RPS11B promoter, by removing the Rap1 consensus sites.
conclusionsThe presence of transcription factor-binding motifs is an important determinant of nucleosome depletion. Most motifs are associated with marked depletion only when they appear in combination, consistent with a model in which transcription factors act collaboratively to exclude nucleosomes and gain access to target sites in the DNA. In contrast, Rap1-binding sites cause marked depletion under steady-state conditions. We speculate that nucleosome depletion enables Rap1 to define chromatin domains and alter them in response to environmental cues.
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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.