How short is short in RNAi Research

The original work of Mello and Fire from the Univ. of Massachusetts demonstrated in C. elegans, that gene expression is controlled by RNA interference (RNAi) . The initial patent applications filed by the Univ. of Massachussetts, with both Mello and Fire as the inventors, and covering this use of RNAi, clained only dsRNA longer than 25 bp’s. Later on, work done in mamalians showed that the long ds RNA was capable of inducing the release of IFN and other pro-inflammatory cytokines, causing dangerous reactions in the animals we tested. We now know that long dsRNA is recognized in the endosomes by TLRs, inducing an undesirable immune response in the animals; a situation that created a new challenge in the study of RNAi. Subsequently other researchers, such as Tuschl et.al. now at Rockefeller Univ, realized that shorter dsRNAi fragments of 25bp of smaller, while still capable of inhibiting the expression of a targeted gene, failed to induce an innate immunity response. In other words, the mammalian system is still capable of utilizing the diced dsRNA produced by the enzyme Dicer, which normally chops down the long dsRNA to sizes of 21-23 nts with 2 bases overhanging at the 3’ends of each strand. These 2 bases overhanging in dsRNA suggests that perhaps Dicer cleaves the long dsRNA in a fashion analogous to restriction enzymes. This short dsRNA can then interact with the RISC complex, where the guide strand is prepared and readied up to base pair with the target mRNA for its cleavage.

The RNAi situation is a good example of the unexpected in science. Although at the time of the initial discovery it was hard to predict that very small fragments of RNA could be pivotal in such important newly found mechanism, currently, even shorter dsRNA fragments, e.g. 15-18 bps’ are being tested. These new third generation modifiers such as LNA’s, UNA’s and others, because of their size have significant therapeutic potential.

There is a significant amount of ongoing research to elucidate the fine details of this novel gene control mechanism, including but not limited to studies of how miRNA precursors are transported to specific compartments of the cell, as these events may play important roles in the processing of the precursor by Dicer to render the active mature form of dsRNA.