Functional Proximity across an mRNA

Extensive RNA-protein interactions occur throughout the lifecycle of an mRNA that up- and down-regulate mRNA translation and degradation. Modulating interactions between regulatory proteins and mRNAs can have large effects on gene expression and might be useful for creating therapeutic manipulations, especially for difficult-to-drug proteins. Here, we directed three degradation-inducing proteins that normally bind the 5′ cap, 3′-untranslated region (UTR), or 3′ poly(A) tail to unconventional sites spanning coding and noncoding regions across a reporter mRNA. DCP2, the 5′ decapping enzyme, reduced expression only when targeted to the 5′-UTR. ZFP36L2, a 3′-UTR adapter protein, reduced expression when directed to either the 3′-UTR or the 3′ half of the coding sequence, the latter region outside its conventional site. CNOT7, a catalytic subunit within the CCR4-NOT deadenylase complex, reduced expression when directed anywhere in the mRNA, most strongly at both “ends” in the 5′- and 3′-UTRs. mRNAs can therefore be degraded by directing proteins to positions far from their conventionally understood regulatory sites. Our study reveals extensive through-space functional proximity across an mRNA. These observations have broad implications for understanding large-scale RNA structure and for emerging applications in therapeutically targeted RNA degradation.