Single-molecule modeling of mRNA degradation by miRNA: Lessons from data

TL;DR

This study refines the understanding of miRNA-mediated mRNA degradation at the single molecule level, proposing a new pathway where NOT1 interacts with miRISC before mRNA binding, supported by data analysis.

Contribution

It challenges previous models by proposing an alternative pathway for miRNA-induced mRNA decay, supported by systematic data analysis and experimental insights.

Findings

Only 7% of mRNA regulated by miRNA if previous pathway is correct

NOT1 interacts with miRISC before target mRNA binding

mRNA degradation is slower when miRISC binds alone

Abstract

Recent experimental results on the effect of miRNA on the decay of its target mRNA have been analyzed against a previously hypothesized single molecule degradation pathway. According to that hypothesis, the silencing complex (miRISC) first interacts with its target mRNA and then recruits the protein complexes associated with NOT1 and PAN3 to trigger deadenylation (and subsequent degradation) of the target mRNA. Our analysis of the experimental decay patterns allowed us to refine the structure of the degradation pathways at the single molecule level. Surprisingly, we found that if the previously hypothesized network was correct, only about 7% of the target mRNA would be regulated by the miRNA mechanism, which is inconsistent with the available knowledge. Based on systematic data analysis, we propose the alternative hypothesis that NOT1 interacts with miRISC before binding to the target mRNA. Moreover, we show that when miRISC binds alone to the target mRNA, the mRNA is degraded more slowly, probably through a deadenylation-independent pathway. The new biochemical pathway we propose both fits the data and paves the way for new experimental work to identify new interactions.