Frequency response in microRNA-mediated genetic regulation

SZISCHIK CANDELA; FERRO ELSI ; BOSIA CARLA; ALEJANDRA C VENTURA

Milam

Workshop; CAMBI (Computational Aspects and Modeling of Biological Information) Workshop; 2022

EU-supported INFERNET project

Livingcells are inherently dynamic. Live-cell time-lapse microscopy and fluorescentreportergenes have allowed to track the dynamic behavior of molecules over time,therebyuncovering a picture where many regulatory proteins undergo pulses ofactivation anddeactivation. Oscillatory signals are able to carry key biologicalinformationencoded in the shape of pulses, where its features such as the duration,frequencyand amplitude can determine the behavior of signaling pathways.Specifically,some circuits have been shown to respond preferentially to certainoscillationfrequencies. MicroRNAs, small RNA molecules that regulate their targetmessengerRNA (mRNA) through a post-transcriptional mechanism, have beenfound to beexpressed in pulses. MiRNAs repress gene expression by promoting thedegradationof target mRNA and/or inhibiting its translation. Regulatory circuitsinvolvingmiRNAs are increasingly being uncovered acting in key biologicalprocesses,such as development and differentiation. MiRNAs play fundamental rolesinpathological contexts related to tumorigenesis, viral infection, andneurologicaldiseases. Asingle miRNA regulates multiple target genes, thereby generatingcompetitionbetween target mRNAs. However, the interplay between competition andpulsatilesignaling is poorly understood. Moreover, an mRNA molecule often presentsmultiplebinding sites relative to a specific miRNA, making the extent of repressiondependenton how many of such sites are bound and thus conferring cooperativepropertiesto the interaction between a miRNA and its target. We theoreticallyaddresspulsatile signaling within miRNA-mediated regulation focusing on the role ofoscillationfrequency and investigating its interplay with significant features of miRNA-mRNAinteraction, namely cooperative binding and competition between targets. Ourresultsindicate that modulation of some parameters that control competition andcooperativitycould serve as a tuning mechanism: it can shift and sharpen thefrequencypreference response, leading to non-intuitive effects. These results canalso beaddressed experimentally by quantifying target fold-repression by time-lapsemicroscopyand using optogenetics to induce a pulsatile miRNA expression andtransfecting fluorescent targets.