Translation affects mRNA stability in a codon-dependent manner in human cells

Elife. 2019 Apr 23:8:e45396. doi: 10.7554/eLife.45396.


mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.

Keywords: SLAM-seq; chromosomes; codon optimality; gene expression; human; mRNA stability; poly(A)-tail; tRNA; translation; zebrafish.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Codon*
  • Humans
  • Protein Biosynthesis*
  • RNA Stability*


  • Codon

Associated data

  • GEO/GSE126523
  • GEO/GSE59717
  • GEO/GSE95683
  • GEO/GSE97259
  • GEO/GSE54114
  • GEO/GSE52809

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.