ArticleProceedings of the National Academy of Sciences of the United States of America2014
Protein-DNA binding in the absence of specific base-pair recognition.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
70 citing papers in PubMed, 127 citations in OpenAlex.
- Article
- Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor.Nature communications · 2025Article
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms.Briefings in bioinformatics · 2025Article
- Bimodal specificity of TF-DNA recognition in embryonic stem cells.Nucleic acids research · 2025Article
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- The emergence and evolution of gene expression in genome regions replete with regulatory motifs.eLife · 2024Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- Noncanonical binding of transcription factors: time to revisitMolecular biology of the cell · 2023Review
- Article
- RNAP Promoter Search and Transcription Kinetics in LiveThe journal of physical chemistry. B · 2023Article
- Interplay Between Polymorphic Short Tandem Repeats and Gene Expression Variation in Caenorhabditis elegans.Molecular biology and evolution · 2023Article
- Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.Journal of evolutionary biology · 2023Review
- Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.Biophysical journal · 2022Article
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution.Molecular psychiatry · 2022Review
- The Limitation of the Combination of Transition State Theory and Thermodynamics for the Reactions of Proteins and Nucleic Acids.Biomolecules · 2021Article
- Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model.Nucleic acids research · 2021Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)-DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF-DNA binding preferences. We used high-throughput protein-DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein-DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein-DNA binding preferences.
Indexed as
Identifiers
What OpenQuestion holds
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.