ArticleBiophysical journal2013
Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
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- 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
- Article
- One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism.Scientific reports · 2021Article
- Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences.Biomolecules · 2020Article
- Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.Molecules (Basel, Switzerland) · 2018Article
- Energetic funnel facilitates facilitated diffusion.Nucleic acids research · 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
- 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
- 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
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent experiments provide an unprecedented view of protein-DNA binding in yeast and human genomes at single-nucleotide resolution. These measurements, performed over large cell populations, show quite generally that sequence-specific transcription regulators with well-defined protein-DNA consensus motifs bind only a fraction among all consensus motifs present in the genome. Alternatively, proteins in vivo often bind DNA regions lacking known consensus sequences. The rules determining whether a consensus motif is functional remain incompletely understood. Here we predict that genomic background surrounding specific protein-DNA binding motifs statistically modulates the binding of sequence-specific transcription regulators to these motifs. In particular, we show that nonconsensus protein-DNA binding in yeast is statistically enhanced, on average, around functional Reb1 motifs that are bound as compared to nonfunctional Reb1 motifs that are unbound. The landscape of nonconsensus protein-DNA binding around functional CTCF motifs in human demonstrates a more complex behavior. In particular, human genomic regions characterized by the highest CTCF occupancy, show statistically reduced level of nonconsensus protein-DNA binding. Our findings suggest that nonconsensus protein-DNA binding is fine-tuned around functional binding sites using a variety of design strategies.
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