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This paper describes differential transcript usage as

Differential transcript usage (DTU) is a special case of alternative splicing in which a gene’s relative transcript abundance (RTA) profile, the proportion of total gene-level expression that arises from each of the gene’s transcript isoforms, differs between conditions (Soneson et al., 2016). [...] An example of DTU may be illustrated by the scenario where the total gene expression is the same between conditions A and B, but transcript isoform 1 is the predominantly expressed transcript in condition A while transcript isoform 2 is the predominantly expressed transcript in condition B.

My question is: is differential transcript usage essentially the same as the usage levels of particular codons? If not, what is the difference? I am unsure of what "transcript isoforms" are, so I'm not sure whether it's talking about codons here or something entirely different.

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No, it is a completely different thing, which has to do with splicing and alternative splicing.

I refer you to some genetics text for details on splicing and alternative splicing, but I will give here a very brief and incomplete explanation fo what they are and how they fint into DTU.

Genes are composed of introns and exons. Exons are the only parts of genes that are usually composing the mature transcript (intron retention is possible, but we are not interested in that). Splicing is the mechanism by which in a eukaryotic gene, introns are removed, and the mature transcript is assembled only using exons. During splicing, not all exons are necessarily retained. Imagine a gene with exons 1, 2 and 3. It is possible that the main form (called isoform) is the one consisting of exons 1, 2 and 3. Let's call that Isoform 1. However, due to a phenomenon called alternative splicing, other isoforms, can be generated, for example one isoform composed by exons 1 and 3. Let's call that Isoform 2. On average, we may imagin that the abundance of Isoform 1 compared to Isoform 2 is rather constant. However, some treatments or some changes in environmental stimuli, can give rise to a Differential Transcript Usage by which the relative abundance of the two isoforms changes.

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  • $\begingroup$ Thanks, but doesn't codon usage bias directly affect splicing, which directly impacts differential transcript usage due to evolutionary selection/pressure for certain isoforms over others? Would it be possible to update your answer relative to what's written in the "Patterns across a gene" section of nature.com/articles/nrg2899, specifically the first paragraph part that ends with "...in shaping codon usage near intron–exon boundaries". There seems to be a lot more nuance here than first meets the eye. $\endgroup$ – npark Feb 8 at 20:19
  • $\begingroup$ I would say it's true codon usage could affect splicing, but that's mostly for comparing across species. In the same species, the codon is the same for a given gene, therefore it has nothing to do regulating alternative splicing. Differential transcript usage under different conditions should be regulated by other factors. $\endgroup$ – Phoenix Mu Feb 19 at 18:16

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