ArticleMolecular biology and evolution2014
Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 17 citations in OpenAlex.
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- Estimating the Distribution of Fitness Effects in Aye-Ayes (Daubentonia madagascariensis), Accounting for Population History as Well as Mutation and Recombination Rate Heterogeneity.American journal of primatology · 2025Article
- Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.bioRxiv : the preprint server for biology · 2024Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Genetic modification of miR-34a enhances efficacy of transplanted human dental pulp stem cells after ischemic stroke.Neural regeneration research · 2023Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.Nucleic acids research · 2017Article
- Evolutionary Transitions of MicroRNA-Target Pairs.Genome biology and evolution · 2016Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifted dramatically, sometimes over very brief periods of evolutionary time. To determine whether the functions of conserved miRNAs are stable or dynamic over evolutionary time scales, we have here defined the neutral turnover rates of short sequence motifs in predicted primate 3'-UTRs. We find that commonly used approaches to quantify motif turnover rates, which use a presence/absence scoring in extant lineages to infer ancestral states, are inherently biased to infer the accumulation of new motifs, leading to the false inference of continually increasing regulatory complexity over time. Using a maximum likelihood approach to reconstruct individual ancestral nucleotides, we observe that binding sites of conserved miRNAs in fact have roughly equal numbers of gain and loss events relative to ancestral states and turnover extremely slowly relative to nearly identical permutations of the same motif. Contrary to case studies showing examples of functional turnover, our systematic study of miRNA binding sites suggests that in primates, the regulatory roles of conserved miRNAs are strongly conserved. Our revised methodology may be used to quantify the mechanism by which regulatory networks evolve.
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