Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

TLDR

MicroRNAs regulate gene expression through deadenylation, repression, and mRNA decay, yet the relative contribution of each mechanism in dynamic contexts remains unclear. The study monitored miR‑430’s effect on ribosome occupancy of endogenous mRNAs in zebrafish embryos to determine whether translation is repressed before mRNA decay. The results show that miR‑430 reduces ribosome occupancy by inhibiting initiation before mRNA decay, with translational repression occurring prior to deadenylation and ribosome density remaining uniform along the transcript.

Abstract

MicroRNAs regulate gene expression through deadenylation, repression, and messenger RNA (mRNA) decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild-type and dicer mutant zebrafish embryos and found that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation with use of an internal polyadenylate tail did not block target repression. Lastly, we observed that ribosome density along the length of the message remains constant, suggesting that translational repression occurs by reducing the rate of initiation rather than affecting elongation or causing ribosomal drop-off. These results show that miR-430 regulates translation initiation before inducing mRNA decay during zebrafish development.