Post-doctoral opening at CABD-Seville

In our local fish community at the CABD we are currently using both morpholinos and now CRISPr approaches. Recently, we have discussed the paper published in Developmental Cell by Kok et. al. (Lawson’s group), which concerns the poor correlation between mutant and MO-induced phenotypes. All the people participating in the journal club agreed on the general consensus of MO-based studies potentially leading to “false positives”, and the discussion “Mutants vs Morphants” proceeded along the same lines of Asilomar’s discussion (see Jon Moulton post above). However I would like to comment here on a particular aspect of this issue that I think may be important. That is, the unclear molecular nature of the MOs off-target effects. Are these off-target effects due to interference with specific off-target genes? If this were the case, a broad range of “fake phenotypes” should be expected as the off-target effects would depend on the specific sequence of the MO injected. In an alternative hypothesis, off-target effects may derive from sequence-independent interference with general gene expression mechanisms (either RNA-dependent or not). I personally feel that the list of the “fake” MOs-induced phenotypes described in Kok’s paper (i.e. ISV stalling, gastrulation defects, short axis, curved trunk, heart edema, necrosis, etc.) does not represents the full spectrum of the MO-induced phenotypes described in the literature. This observation supports the notion of a sequence-independent false positive effect. As an example, very little is known about the mechanism by which MOs induce p53 activation. These global effects on translation, splicing, etc., which is indeed discussed in Kok’s paper, may have important consequences on the evaluation of the specificity of a MO-induced phenotype. Whereas certain phenotypes may be frequently induced by MO injection (i.e. short axis, heart edema, stalled ISV, etc.), suggesting an off-target effect, other “unusual” phenotypes may serve as an indication of gene-specific interference (provided that all the necessary controls are also included in the study, of course).