ArticlePloS one2011
Occlusion of regulatory sequences by promoter nucleosomes in vivo.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- Structural Plasticity of Pioneer Factor Sox2 and DNA Bendability Modulate Nucleosome Engagement and Sox2-Oct4 Synergism.Journal of molecular biology · 2023Article
- Nucleosomal proofreading of activator-promoter interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Epigenetic Regulation of S100A9 and S100A12 Expression in Monocyte-Macrophage System in Hyperglycemic Conditions.Frontiers in immunology · 2020Article
- Design principles for nuclease-deficient CRISPR-based transcriptional regulators.FEMS yeast research · 2018Review
- An Essential Viral Transcription Activator Modulates Chromatin Dynamics.PLoS pathogens · 2016Article
- Mapping nucleosome positions using DNase-seq.Genome research · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting.Genes · 2015Review
- Nucleosomal promoter variation generates gene expression noise.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Nucleosomes, transcription, and probability.Molecular biology of the cell · 2014Article
- The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin.Nucleic acids research · 2014Review
- Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae.Nucleic acids research · 2014Article
- Article
- Linking stochastic fluctuations in chromatin structure and gene expression.PLoS biology · 2013Article
- Article
- Disentangling the many layers of eukaryotic transcriptional regulation.Annual review of genetics · 2012Review
- A chemical approach to mapping nucleosomes at base pair resolution in yeast.Methods in enzymology · 2012Article
- In vivo role for the chromatin-remodeling enzyme SWI/SNF in the removal of promoter nucleosomes by disassembly rather than sliding.The Journal of biological chemistry · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Nucleosomes are believed to inhibit DNA binding by transcription factors. Theoretical attempts to understand the significance of nucleosomes in gene expression and regulation are based upon this assumption. However, nucleosomal inhibition of transcription factor binding to DNA is not complete. Rather, access to nucleosomal DNA depends on a number of factors, including the stereochemistry of transcription factor-DNA interaction, the in vivo kinetics of thermal fluctuations in nucleosome structure, and the intracellular concentration of the transcription factor. In vitro binding studies must therefore be complemented with in vivo measurements. The inducible PHO5 promoter of yeast has played a prominent role in this discussion. It bears two binding sites for the transcriptional activator Pho4, which at the repressed promoter are positioned within a nucleosome and in the linker region between two nucleosomes, respectively. Earlier studies suggested that the nucleosomal binding site is inaccessible to Pho4 binding in the absence of chromatin remodeling. However, this notion has been challenged by several recent reports. We therefore have reanalyzed transcription factor binding to the PHO5 promoter in vivo, using 'chromatin endogenous cleavage' (ChEC). Our results unambiguously demonstrate that nucleosomes effectively interfere with the binding of Pho4 and other critical transcription factors to regulatory sequences of the PHO5 promoter. Our data furthermore suggest that Pho4 recruits the TATA box binding protein to the PHO5 promoter.
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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.