SUMMARYMany siRNAs and shRNAs are toxic to cancer cells through a 6mer seed sequence (position 2-7 of the guide strand). A siRNA screen with all 4096 possible 6mer seed sequences in a neutral RNA backbone revealed a preference for guanine in positions 1-3 and a GC content of >80% of the 6mer seed in the most toxic siRNAs. These 6mer seed containing siRNAs exert their toxicity by targeting survival genes which contain GC-rich 3'UTRs. The master tumor suppressor miRNA miR-34a was found to be toxic through such a G-rich 6mer seed suggesting that certain tumor suppressive miRNAs use a toxic 6mer seed to kill cancer cells. An analysis of all mature miRNAs suggests that most miRNAs evolved to avoid guanine at the 5' end of the 6mer seed sequence of the predominantly expressed arm. In contrast, for many tumor suppressive miRNAs the predominant arm contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells.
INTRODUCTIONRNA interference (RNAi) is a form of post-transcriptional regulation exerted by 19-21nt long double stranded RNAs that represses expression of target mRNAs that harbor reverse complementarity to the antisense/guide strand of the small RNA. This results in degradation of the targeted mRNA or in translational repression. RNAiactive guide RNAs can be endogenous siRNAs and micro(mi)RNAs. For a miRNA, the RNAi pathway begins in the nucleus with transcription of a primary miRNA precursor (pri-miRNA) . Pri-miRNAs are first processed by the Drosha/DGCR8 Microprocessor complex into pre-microRNAs which are exported from the nucleus to the cytoplasm by Exportin 5 (Yi, Qin, Macara, & Cullen, 2003). Once in the cytoplasm, Dicer processes them further (Bernstein, Caudy, Hammond, & Hannon, 2001;Hutvagner et al., 2001) and these mature dsRNA duplexes are then loaded into Argonaute (Ago) proteins to form the RNAinduced silencing complex (RISC) (Y. Wang, Sheng, Juranek, Tuschl, & Patel, 2008). The sense/passenger strand is ejected/degraded, while the guide strand remains associated with the RISC (Leuschner, Ameres, Kueng, & Martinez, 2006). While si/shRNAs are usually designed with 100% reverse complementarity to their intended targets and induce AGO2 dependent target degradation (Schirle & MacRae, 2012), cleavageindependent RNAi as exerted by miRNAs causes deadenylation/degradation or translational repression via interaction between AGO2 and TNRC6 family proteins that in turn recruit the CCR4-NOT deadenylase complex (Eulalio, Huntzinger, & Izaurralde, 2008). RNAi can be initiated with as little as six nucleotide basepairing between a guide RNA's so-called seed sequence (positions 2 to 7) and the target RNA (Lai, 2002;Lewis, Shih, Jones-Rhoades, Bartel, & Burge, 2003). This seed-based targeting is restricted to binding sites located in the 3'UTR of a target mRNA (Baek et al., 2008;Selbach et al., 2008). miRNAs play important roles in cancer (Esquela-Kerscher & Slack, 2006). While the function of a miRNA depends on the nature of its targets, some miRNA families have predominantly tumor suppressive or oncogenic...