Year: 2022

CODONS. “The nucleotide triplet that codes an amino acid is called a codon. A codon consists of three nucleotides. Three nucleotides per codon are needed to code 20 amino acids; since there are 64 combinations of 4 nucleotides taken three at a time and only 20 amino acids, the code is degenerate (more than one codon per amino acid, in most cases).” https://lnkd.in/dTpzG-s View in LinkedIn

HISTORICAL DOGMA. "Synonymous sites are then the collection of potential synonymous mutations present in a gene. Predicated on the assumption that the coding sequences of a gene is simply the recipe for making the protein, synonymous mutations were long thought to have no functional effect, in other words to be “silent” and thus selectively neutral." https://lnkd.in/dU2Q65U View in LinkedIn

CODON BIAS. "Highly expressed genes and codons encoding functionally important amino acids generally display particularly biased patterns of codon usage. This observation led to the theory that selection for translation optimization generates higher levels of codon bias. In other words, it is thought that the speed and accuracy of mRNA translation is higher for a subset of codons, referred to as “optimal” (“preferred”) codons." https://lnkd.in/dU2Q65U View in LinkedIn

PREFERRED CODONS. "Such codons are translated more accurately and more efficiently because they are recognized by more abundant tRNA molecules with more specific anti-codon binding. While this kind of selection acting on synonymous mutations is widely accepted, it is generally estimated to be weak - nearly, if not quite, neutral." https://lnkd.in/dU2Q65U View in LinkedIn

STILL CONSIDERED NEUTRAL. "Synonymous variation is therefore still often thought to lack any major functional or evolutionary importance." https://lnkd.in/dU2Q65U View in LinkedIn

CONTRADICTORY DATA. "Experimental evidence from a wide range of species substantiates an important functional role for synonymous sites." https://lnkd.in/dU2Q65U View in LinkedIn

NOT NEUTRAL. "Recent studies have uncovered a myriad of different types of functional information encoded into the coding sequence of genes beyond the protein recipe, including controls for translational efficiency and accuracy, splicing enhancers, micro-RNA binding, nucleosome positioning, and more." https://lnkd.in/dU2Q65U View in LinkedIn

NEW PARADIGM. "With the discovery of a significant fraction of sites under strong constraint in Drosophila, two things become clear: the role of synonymous sites in the biology of genomes is far greater than the neutral, “silent” part they were once assumed to play; and we still have much to learn about the functionality encoded in genes." https://lnkd.in/dU2Q65U View in LinkedIn

SEA CHANGE. "The majority of the human genome is dynamically transcribed into RNA, most of which does not code for proteins. The once common presumption that most non–protein-coding sequences are nonfunctional for the organism is being adjusted to the increasing evidence that noncoding RNAs (ncRNAs) represent a previously unappreciated layer of gene expression essential for the epigenetic regulation of differentiation and development." https://lnkd.in/guFKNHU View in LinkedIn

SECONDARY STRUCTURES. "Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function." http://nar.oxfordjournals.org/content/early/2013/07/11/nar.gkt596.full View in LinkedIn