Quantification of mRNA Decay Rates in HeLa and SH-SY5Y Cell Lines Reveals Novel Properties of Membrane Protein Coding Transcripts

Abstract

Posttranscriptional regulation is crucial for siRNA design, as decay rates in cell lines influence perceived siRNA potency. This study profiles transcripts with ‘fast’ and ‘slow’ half-lives in HeLa and SH-SY5Y cells, commonly used in drug discovery. We calculated half-lives for 1,815 HeLa and 5,376 SH-SY5Y transcripts, finding comparable half-lives between cell lines, though HeLa cells generally had longer half-lives. Comparing mRNA and protein half-lives, ‘fast’ decay transcripts encoded proteins with shorter half-lives, while ‘slow’ decay transcripts encoded stable proteins. We linked mRNA decay rates to siRNA activity by comparing HeLa data to a previous siRNA screen, discovering that faster decay transcripts had lower knockdown. Surprisingly, stable transcripts, more amenable to knockdown, were over-represented by membrane protein-coding transcripts. Despite their stability, these transcripts had low-to-moderate expression, regardless of miRNA regulation. We explored cis- and trans- features affecting mRNA stability and expression, suggesting that low RNA binding protein (RBP) binding, combined with specific stabilizing RBP regulation, contributes to the stability of these membrane protein-coding transcripts. This study highlights the importance of understanding transcript features, mRNA decay and its potential impact on siRNA efficacy, particularly for transcripts encoding membrane proteins.