ArticleBiophysical journal2012
Nonspecific protein-DNA binding is widespread in the yeast genome.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Following the tracks: How transcription factor binding dynamics control transcription.Biophysical journal · 2022Review
- The Limitation of the Combination of Transition State Theory and Thermodynamics for the Reactions of Proteins and Nucleic Acids.Biomolecules · 2021Article
- Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock.Biophysical journal · 2021Article
- One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism.Scientific reports · 2021Article
- Article
- Nanoparticle-Based Proximity Ligation Assay for Ultrasensitive, Quantitative Detection of Protein Biomarkers.ACS applied materials & interfaces · 2018Article
- Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.Molecules (Basel, Switzerland) · 2018Article
- Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences.Transcription · 2018Article
- Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.The journal of physical chemistry letters · 2017Article
- Article
- Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.PLoS computational biology · 2015Article
- Protein-DNA binding in high-resolution.Critical reviews in biochemistry and molecular biology · 2015Review
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding.Biophysical journal · 2013Article
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Authors and funding
2 authors.
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Abstract
Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis-regulatory code of a eukaryotic genome. Here, we show that nonspecific transcription factor (TF)-DNA binding significantly influences binding preferences of the majority of transcription regulators in promoter regions of the yeast genome. We show that promoters of SAGA-dominated and TFIID-dominated genes can be statistically distinguished based on the landscape of nonspecific protein-DNA binding free energy. In particular, we predict that promoters of SAGA-dominated genes possess wider regions of reduced free energy compared to promoters of TFIID-dominated genes. We also show that specific and nonspecific TF-DNA binding are functionally linked and cooperatively influence gene expression in yeast. Our results suggest that nonspecific TF-DNA binding is intrinsically encoded into the yeast genome, and it may play a more important role in transcriptional regulation than previously thought.
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