A structural interpretation of the effect of GC-content on efficiency of RNA interference

Abstract

BackgroundRNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNAi efficiency, and it is of interest to have a convincing mechanistic interpretation of this observation. We here examine this issue by considering the secondary structures for both the target messenger RNA (mRNA) and the siRNA guide strand.ResultsBy analyzing a unique homogeneous data set of 101 shRNAs targeted to 100 endogenous human genes, we find that: 1) target site accessibility is more important than GC-content for efficient RNAi; 2) there is an appreciable negative correlation between GC-content and RNAi activity; 3) for the predicted structure of the siRNA guide strand, there is a lack of correlation between RNAi activity and either the stability or the number of free dangling nucleotides at an end of the structure; 4) there is a high correlation between target site accessibility and GC-content. For a set of representative structural RNAs, the GC content of 62.6% for paired bases is significantly higher than the GC content of 38.7% for unpaired bases. Thus, for a structured RNA, a region with higher GC content is likely to have more stable secondary structure. Furthermore, by partial correlation analysis, the correlation for GC-content is almost completely diminished, when the effect of target accessibility is controlled.ConclusionThese findings provide a target-structure-based interpretation and mechanistic insight for the effect of GC-content on RNAi efficiency.

Dimeric artificial microRNAs mediate high resistance to RSV and RBSDV in transgenic rice plants

“…This finding suggested that the free energies of amiRNAs might be not the main factor that determines the resistance level of transgenic plants. This is consistent with other studies that demonstrated a lack of correlation between amiRNA (or siRNA) activity and DG (Chan et al 2009;Song et al 2014;Zhang et al 2013).…”

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

“…GC content has a rare relationship with replication timing in human genome (38). GC content also have an effect on RNAi, because it is highly correlated to RNAi target site accessibility and negatively correlated with RNAi activity (39).…”

A Computational Approach to Design Potential Antiviral RNA for 3’UTR Post Transcriptional Gene Silencing of Different Strains of Zika Virus

“…siRNA with GC content within the range of 31.6% -57.9%, is usually recommended due to its negative correlation between GC-content and RNAi activity. 44 Four predicted consensus siRNA have found within the range of recommended GC content. The free energy of folding is a significant parameter that illustrates the stability of designed siRNA.…”