ArticleBiophysical journal2013
Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 24 citations in OpenAlex.
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.Biophysical journal · 2022Article
- The Limitation of the Combination of Transition State Theory and Thermodynamics for the Reactions of Proteins and Nucleic Acids.Biomolecules · 2021Article
- One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism.Scientific reports · 2021Article
- Energetic funnel facilitates facilitated diffusion.Nucleic acids research · 2018Article
- Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences.Transcription · 2018Article
- Specificity-Determining DNA Triplet Code for Positioning of Human Preinitiation Complex.Biophysical journal · 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
- Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.PLoS computational biology · 2016Article
- The Determinants of Directionality in Transcriptional Initiation.Trends in genetics : TIG · 2016Review
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.Nucleic acids research · 2016Article
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.PLoS computational biology · 2015Article
- Functional roles of nucleosome stability and dynamics.Briefings in functional genomics · 2015Review
- Protein-DNA binding in the absence of specific base-pair recognition.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.Nucleic acids research · 2014Article
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Mechanisms of protein binding to DNA: statistical interactions are important.Biophysical journal · 2013Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide binding preferences of the key components of eukaryotic preinitiation complex (PIC) have been recently measured at high resolution in Saccharomyces cerevisiae by Rhee and Pugh. However, the rules determining the PIC binding specificity remain poorly understood. In this study, we show that nonconsensus protein-DNA binding significantly influences PIC binding preferences. We estimate that such nonconsensus binding contributes statistically at least 2-3 kcal/mol (on average) of additional attractive free energy per protein per core-promoter region. The predicted attractive effect is particularly strong at repeated poly(dA:dT) and poly(dC:dG) tracts. Overall, the computed free-energy landscape of nonconsensus protein-DNA binding shows strong correlation with the measured genome-wide PIC occupancy. Remarkably, statistical PIC preferences of binding to both TFIID-dominated and SAGA-dominated genes correlate with the nonconsensus free-energy landscape, yet these two groups of genes are distinguishable based on the average free-energy profiles. We suggest that the predicted nonconsensus binding mechanism provides a genome-wide background for specific promoter elements, such as transcription-factor binding sites, TATA-like elements, and specific binding of the PIC components to nucleosomes. We also show that nonconsensus binding has genome-wide influence on transcriptional frequency.
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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.