A New miRNA Motif Protects Pathways Expression in Gene Regulatory Networks

The continuing discovery of new functions and classes of small non-coding RNAs is suggesting the presence of regulatory mecha- nisms far more complex than the ones identied so far. In our compu- tational analysis of a large set of public available databases, we found statistical evidence of an inter-pathway regulatory motif, not previously described, that reveals a new protective role miRNAs may play in the successful activation of a pathway. This paper reports the main outcomes of this analysis. the central role of non-coding RNAs in intra-pathway regulation (2). In our research for higher- level mechanisms of transcriptional regulation, we identied an inter-pathway regulatory motif, not previously described, in which miRNAs seem to play a new role in the successful expression of a pathway. In particular, some intragenic miRNAs, co-expressed with one or more pathway genes, seem to act as pathway protectors. We observed that, in several situations, they target the transcription factors of a set of genes hosting miRNAs that could interfere with the pathway successful activation. We found statistical evidence that this inter-pathway reg- ulatory motif, which we called Pathway Protection Loop (PPL), is very common in several classes of KEGG pathways (7). Figure 1 shows the structure of a PPL. The successful full activation of a pathway not only depends on the correct expression of the pathway genes, but also on controlling the expression of other genes that could potentially dysregu- late (down-regulate or silence) the pathway at some point. We call these genes the Pathway Antagonist Genes (PAGs). A possible way PAGs may interfere with the activity of a pathway is to express a set of miRNAs, in this context called An- tagonist miRNAs, targeting and down-regulating some of the pathway's genes. Interestingly, we discovered that, in several situations, the pathway intragenic miRNAs target and silence the transcription factors of the PAGs, thus creating