Off-target messenger RNAs with partial complementarity to siRNA seed region (siRNA off-targets)

Off-target messenger RNAs with partial complementarity to the siRNA seed region refer to a broad set of unintended transcripts that are downregulated by small interfering RNA (siRNA) drugs. This effect is primarily mediated by the seed region of the siRNA guide strand (nucleotides 2 through 8), which can bind to the 3' untranslated regions (UTRs) of mRNAs with only partial complementarity (Jackson et al., 2003). This interaction mimics the endogenous microRNA (miRNA) pathway, leading to the recruitment of the RNA-induced silencing complex (RISC) and subsequent translational repression or mRNA decay of the unintended transcript (Birmingham et al., 2006). Because the seed sequence is short, a single siRNA can potentially interact with hundreds of off-target mRNAs, leading to unintended biological effects or toxicity (Janas et al., 2018). To mitigate these risks, therapeutic siRNAs are often engineered with chemical modifications, such as 2'-O-methyl (2'-OMe) substitutions at position 2 of the guide strand, to destabilize off-target binding without compromising on-target activity (Setten et al., 2019). Understanding and predicting these off-target profiles is a critical component of the safety assessment for RNAi-based therapeutics like Patisiran and Inclisiran.

Other names

Seed-mediated off-targetsmiRNA-like off-target effectssiRNA off-target effectsUnintended mRNA targets

siRNAs loaded into the RNA-induced silencing complex (RISC) bind to unintended mRNAs via partial complementarity of the seed region (nucleotides 2-8), leading to miRNA-like translational repression or mRNA decay (Jackson et al., 2003; Birmingham et al., 2006).