ArticleJournal of molecular evolution2006
Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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.
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Who cites it
27 citing papers in PubMed.
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution.Molecular neurobiology · 2025Article
- Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.Nature communications · 2025Article
- Somatic synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma.BMC medical genomics · 2020Article
- Computational Network Analysis Identifies Evolutionarily Conserved miRNA Gene Interactions Potentially Regulating Immune Response in Bovine Trypanosomosis.Frontiers in microbiology · 2019Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Depletion of somatic mutations in splicing-associated sequences in cancer genomes.Genome biology · 2017Article
- ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?Biology direct · 2017Article
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution.Molecular biology and evolution · 2017Article
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- The functional relevance of somatic synonymous mutations in melanoma and other cancers.Pigment cell & melanoma research · 2015Review
- Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs.Molecular biology and evolution · 2015Article
- Decoding mechanisms by which silent codon changes influence protein biogenesis and function.The international journal of biochemistry & cell biology · 2015Review
- Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation.Genome research · 2013Article
- miR-1279, miR-548j, miR-548m, and miR-548d-5p binding sites in CDSs of paralogous and orthologous PTPN12, MSH6, and ZEB1 Genes.BioMed research international · 2013Article
- Biological basis of miRNA action when their targets are located in human protein coding region.PloS one · 2013Article
- Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana.Evolutionary bioinformatics online · 2012Article
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.Genome research · 2011Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Despite prior claims to the contrary, several lines of evidence suggest that selection acts on synonymous mutations in mammals. What might be the mechanisms for such selection? Here I attempt to quantify the constraints on the evolution of the coding sequence resulting from regulation of mRNA by microRNAs (miRNAs) that antisense-bind to the coding region of mRNAs. I employ a set of genes recently experimentally verified to be the target of a miRNA, all with putative antisense pairing domains within the coding sequence. Although very small ( approximately 22 nucleotides), 2 of 13 pairing domains show evidence of significantly slow sequence evolution. This, along with evidence that these genes are regulated by the miRNA under consideration, provides the first good candidate domains for intra-CDS pairing of a miRNA in mammals. When analyzed en masse, the putative pairing domains have a significantly reduced rate of synonymous evolution (approximately 35% lower than null). However, given the size and rarity of pairing domains within the coding sequence, the effects that such constraint has on estimates of the mutation rate are small enough to be ignored (probably less than 1% reduction). The pairing sites also have low Ka values and the selection on the synonymous sites is unlikely to lead to misleading reports of localized high Ka/Ks ratios.
Indexed as
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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.