Hearing silence: non-neutral evolution at synonymous sites in mammals

By J. Chamary, Joanna L. Parmley, Laurence D. Hurst. Nature reviews genetics, 2006

852 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5335d395c964374b372d7671ab27391f416e4526

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Citations in the corpus

Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. (2007, background): “Although synonymous substitutions were shown not to be completely selectively neutral35–37 (reviewed by Chamary et al.38), the effect on fitness of the vast majority of them in the human population is believed to be relatively small.”
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. (2006, background): “Although synonymous mutations have no effect on the encoded protein, about 40% of such mutations have been opposed by selection, and some of those mutations are involved in diseases (Chamary et al., 2006).”
Toward a Kinetic Understanding of Eukaryotic Translation. (2018, background): “…whereas nonoptimal codons (rare codons) interact with tRNAs that are low in abundance and therefore more slowly accommodated into the A site of the ribosome during elongation (reviewed in Chamary et al. 2006; Plotkin and Kudla 2011; Koutmou et al. 2015; Rodnina 2016; Hanson and Coller 2018).”
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes (2010, background): “Translationally preferred codons are selected for accurate and efficient translation in bacteria, yeast, worm, fly, and even in mammals [2–13].”
Biased gene conversion and the evolution of mammalian genomic landscapes. (2009, background): “One possibility is that synonymous codon positions are under selective pressure (25, 41, 120).”
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution (2008, neutral): “Selection on translational efficiency in mammals is viewed as weak and contentious (Chamary et al., 2006) or absent (dos Reis et al., 2004).”
The rise of regulatory RNA (2014, background): “…205 , but also that protein-coding sequences themselves can have other embedded functions, as suggested by constraints on synonymous codon usage 330,331 , including regulatory functions as epigenetic modulators 203 , tissue-specific enhancers 331,332 and transcription factor binding sites 333 .”
The Genetic Signatures of Noncoding RNAs (2009, background): “This is indicated by the complexity of overlapping sense and antisense coding and noncoding transcripts from most genomic loci [2–5] and evidence that protein-coding sequences are under constraint not only at the amino acid sequence level, but also within their RNA sequence [160].”