Regulatory consequences of mRNA Poly(A)-Tail length changes

Abstract

Eukaryotic mRNAs have a cap structure at their 5' ends and a poly(A) tail at their 3' ends, and the proteins that bind these features increase the stability and translation of an mRNA. The influence of the poly(A) tail on translation was discovered decades ago, but primarily with regard to the idea that an mRNA with a poly(A) tail is better translated than one without. The influence of differences in tail length on translation had been assessed for just a few mRNAs, and in these cases long-tailed mRNAs were better translated than short-tailed mRNAs. We measured the poly(A)-tail length and translational efficiency of mRNAs corresponding to thousands of different genes in 35 different cell types or contexts. Extending previous singlegene studies, we found a global relationship between tail length and translational efficiency in Drosophila oocytes, and Drosophila, Xenopus, and zebrafish embryos. Surprisingly, in all three species, the strong coupling between tail length and translational efficiency was lost once the embryos reached gastrulation, and there was no coupling in the post-embryonic contexts we examined. We thus demonstrated that poly(A)-tail length is a major determinant of translational efficiency during early animal development and discovered a broadly conserved developmental switch in translational control. During the tail-length regulatory regime of the early embryo, a protein or microRNA might regulate translation by changing the poly(A)-tail length of an mRNA, interacting with the translation machinery, or both mechanisms. We characterized the mechanism used by two translational regulatory proteins in Drosophila, finding that they predominantly act by regulating tail length. Likewise, in early zebrafish embryos, microRNAs repress the translation of their hundreds of mRNA targets by shortening poly(A) tails. Our findings indicate that much of the translational regulation in early development is achieved by regulating poly(A)-tail lengths. Outside of early embryonic contexts, microRNAs regulate gene expression by causing both translational repression and mRNA degradation. We greatly expanded the mammalian cell types and contexts in which the steady-state and pre-steady-state effects of a microRNA had been examined globally for endogenous mRNAs. In all post-embryonic contexts with substantial microRNA-mediated repression, the predominant mode of repression was mRNA degradation.