Messenger RNA

Translation (biology)

Nucleotide

Protein secondary structure

Biology

Codon usage bias

Gene

Gene expression

Genome

Peptide sequence

Start codon

Sequence (biology)

Computational biology

Nucleic acid secondary structure

Coding region

Protein primary structure

Cell biology

Translational frameshift

Protein biosynthesis

Genetics

Biochemistry

Proceedings of the National Academy of Sciences

Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used 2 approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs, to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly expressed mRNAs contained a highly structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide variety of primary sequences. Using a set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e., mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.

mRNA structure regulates protein expression through changes in functional half-life