Global 5 '-UTR RNA structure regulates translation of a SERPINA1 mRNA

SERPINA1 mRNAs encode the protease inhibitor alpha-1-antitrypsin and are regulated through post-transcriptional mechanisms. alpha-1-antitrypsin deficiency leads to chronic obstructive pulmonary disease (COPD) and liver cirrhosis, and specific variants in the 5 '-untranslated region (5 '-UTR) are associated with COPD. The NM_000295.4 transcript is well expressed and translated in lung and blood and features an extended 5 '-UTR that does not contain a competing upstream open reading frame (uORF). We show that the 5 '-UTR of NM_000295.4 folds into a well-defined multi-helix structural domain. We systematically destabilized mRNA structure across the NM_000295.4 5 '-UTR, and measured changes in (SHAPE quantified) RNA structure and cap-dependent translation relative to a native-sequence reporter. Surprisingly, despite destabilizing local RNA structure, most mutations either had no effect on or decreased translation. Most structure-destabilizing mutations retained native, global 5 '-UTR structure. However, those mutations that disrupted the helix that anchors the 5 '-UTR domain yielded three groups of non-native structures. Two of these non-native structure groups refolded to create a stable helix near the translation initiation site that decreases translation. Thus, in contrast to the conventional model that RNA structure in 5 '-UTRs primarily inhibits translation, complex folding of the NM_000295.4 5 '-UTR creates a translation-optimized message by promoting accessibility at the translation initiation site.