ArticlePloS one
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors.
Article in PloS one. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed, 13 citations in OpenAlex.
- Core elements play distinct roles in promoter birth and transcriptional regulation.Nature communications · 2026Article
- Decoding and reengineering the promoter specificity of T7-like RNA polymerases based on phage genome sequences.Nucleic acids research · 2025Article
- Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.Briefings in bioinformatics · 2024Article
- ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis.Communications biology · 2023Article
- Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits inACS synthetic biology · 2023Article
- Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.Frontiers in microbiology · 2021Article
- A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana.Nucleic acids research · 2018Article
- Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors.Quantitative biology (Beijing, China) · 2018Article
- Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites.Frontiers in microbiology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to identify and analyze crucial protein-DNA pairs of positions in a family of transcription factors. Correlations are identified by analysis of mutual information between columns of protein and DNA alignments. The algorithm reduces the effects of common phylogenetic history and of abundance of closely related proteins and binding sites. We apply it to five closely related subfamilies of the MerR family of bacterial transcription factors that regulate heavy metal resistance systems. We validate the approach using known 3D structures of MerR-family proteins in complexes with their cognate DNA binding sites and demonstrate that a significant fraction of correlated positions indeed form specific side-chain-to-base contacts. The joint distribution of amino acids and nucleotides hence may be used to predict changes of specificity for point mutations in transcription factors.
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.