Drugs that impair microtubule dynamics alter microtubule-kinetochore attachment and invoke the mitotic checkpoint which arrests cells in mitosis. The arrest can last for hours, but it is leaky: cells adapt (i.e., slip out of it) and exit from mitosis. Here, we investigate the mechanism that allows cells to escape, and whether it is possible to prevent it. Based on a model of the mitotic checkpoint which includes the presence of a positive feedback loop, the escape from the arrest is described as a stochastic transition driven by fluctuations of molecular components from a checkpoint ON to a checkpoint OFF state. According to the model, drug removal further facilitates adaptation, a prediction we confirmed in budding yeast. The model suggests two ways to avoid adaptation: inhibition of APC/C and strengthening the mitotic checkpoint. We confirmed experimentally that both alterations decrease the chance of cells slipping out of mitosis, during a prolonged arrest and after washing out the drug. Our results may be relevant for increasing the efficiency of microtubule depolymerizing drugs.

MOTIVATION: microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions; however, these findings are not easily applicable. RESULTS: We translate this approach into a flexible and user-friendly bioconductor package, scanMiR, also available through a web interface. Using lightweight linear models, scanMiR efficiently scans for binding sites, estimates their affinity and predicts aggregated transcript repression. Moreover, flexible 3'-supplementary alignment enables the prediction of unconventional interactions, such as bindings potentially leading to target-directed microRNA degradation or slicing. We showcase scanMiR through a systematic scan for such unconventional sites on neuronal transcripts, including lncRNAs and circRNAs. Finally, in addition to the main bioconductor package implementing these functions, we provide a user-friendly web application enabling the scanning of sequences, the visualization of predicted bindings and the browsing of predicted target repression. AVAILABILITY AND IMPLEMENTATION: scanMiR and companion packages are implemented in R, released under the GPL-3 and accessible on Bioconductor (https://bioconductor.org/packages/release/bioc/html/scanMiR.html) as well as through a shiny web server (https://ethz-ins.org/scanMiR/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The mitotic checkpoint (also called spindle assembly checkpoint) is a signaling pathway that ensures faithful chromosome segregation. Mitotic checkpoint proteins inhibit the anaphase-promoting complex (APC/C) and its activator Cdc20 to prevent precocious anaphase. Checkpoint signaling leads to a complex of APC/C, Cdc20, and checkpoint proteins, in which the APC/C is inactive. In principle, this final product of the mitotic checkpoint can be obtained via different pathways, whose relevance still needs to be fully ascertained experimentally. Here, we use mathematical models to compare the implications on checkpoint response of the possible pathways leading to APC/C inhibition. We identify a previously unrecognized funneling effect for Cdc20, which favors Cdc20 incorporation into the inhibitory complex and therefore promotes checkpoint activity. Furthermore, we find that the presence or absence of one specific assembly reaction determines whether the checkpoint remains functional at elevated levels of Cdc20, which can occur in cancer cells. Our results reveal the inhibitory logics behind checkpoint activity, predict checkpoint efficiency in perturbed situations, and could inform molecular strategies to treat malignancies that exhibit Cdc20 overexpression.