ReviewJournal of molecular evolution2017
Negative Epistasis in Experimental RNA Fitness Landscapes.
Review in Journal of molecular evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- The distribution of fitness effects during adaptive walks using a simple genetic network.PLoS genetics · 2024Article
- Article
- Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.Nature communications · 2022Article
- A Family of Fitness Landscapes Modeled through Gene Regulatory Networks.Entropy (Basel, Switzerland) · 2022Article
- Dynamic RNA Fitness Landscapes of a Group I Ribozyme during Changes to the Experimental Environment.Molecular biology and evolution · 2022Article
- Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data.Frontiers in molecular biosciences · 2022Article
- Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics.Nature communications · 2021Article
- Fitness landscape of a dynamic RNA structure.PLoS genetics · 2021Article
- A two-step PCR assembly for construction of gene variants across large mutational distances.Biology methods & protocols · 2021Article
- Emerging Frontiers in the Study of Molecular Evolution.Journal of molecular evolution · 2020Article
- High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications.Physical chemistry chemical physics : PCCP · 2020Review
- Recent insights into the genotype-phenotype relationship from massively parallel genetic assays.Evolutionary applications · 2019Review
- Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication.Journal of molecular evolution · 2019Article
- Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase.Journal of molecular biology · 2019Article
- Genotype network intersections promote evolutionary innovation.PLoS biology · 2019Article
- Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA.Journal of the American Chemical Society · 2019Article
- Deep generative models of genetic variation capture the effects of mutations.Nature methods · 2018Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast. The data allow an analysis of the distribution of fitness effects of individual mutations as well as combinations of two or more mutations. Two different approaches to measuring epistasis in the data both reveal a predominance of negative epistasis, such that higher combinations of two or more mutations are typically lower in fitness than expected from the effect of each individual mutation. These data are in contrast to past studies of epistasis that used computationally predicted secondary structures of RNA that revealed a predominance of positive epistasis. The RNA data reviewed here are more similar to that found from mutational experiments on individual protein enzymes, suggesting that a common thermodynamic framework may explain negative epistasis between mutations within macromolecules.
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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.