ArticleScience (New York, N.Y.)2013
Exonic transcription factor binding directs codon choice and affects protein evolution.
Article in Science (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers, 3 of them syntheses that pooled it.
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
159 citing papers in PubMed, 3 syntheses or guidelines pooled it, 288 citations in OpenAlex.
- Transethnic meta-analysis of exome-wide variants identifies new loci associated with male-specific metabolic syndrome.Genes & genomics · 2022Pooled it
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci.Nature genetics · 2016Pooled it
- ERα Micromap (µMap) proximity labeling reveals fulvestrant mechanisms.Nature communications · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- The G→C rs590352 in the Protein-Coding Region of ATXN7L3B Gene Upregulates Its Expression In Vivo.Biochemical genetics · 2026Article
- The exonic SNP rs11676272-C risk allele mediates diet-induced obesity and reduces enhancer activation.EMBO reports · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- NF-κB restrains nutrient-dependent transcription programs through chromatin modulation in Drosophila.Nucleic acids research · 2026Article
- TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.Genetics · 2026Article
- Synonymous editing alters ion channel function, favoring prime editing for retinal disease correction.International journal of biological sciences · 2026Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- A transcription factor ensemble orchestrates bundle sheath expression in rice.Nature communications · 2025Article
- Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.Nature communications · 2025Article
- Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14).Leukemia · 2025Article
- Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks.Cell reports · 2024Article
- Optimization of AAV vectors for transactivator-regulated enhanced gene expression within targeted neuronal populations.iScience · 2024Article
- Functional categorization of gene regulatory variants that cause Mendelian conditions.Human genetics · 2024Review
- In silico validation revealed the role of SCN5A mutations and their genotype-phenotype correlations in Brugada syndrome.Molecular genetics & genomic medicine · 2023Article
- Identification genetic variations in some heat shock protein genes of Tali goat breed and study their structural and functional effects on relevant proteins.Veterinary medicine and science · 2023Article
99 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.
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.