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

Abstract

MicroRNAs regulate gene expression through deadenylation, repression and 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 mutants lacking mature miR-430. We find that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation using an internal poly(A) tail did not block target repression. Finally, we observe 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. In summary, our results show that miR-430 regulates translation initiation before inducing mRNA decay.

Kinetic analysis reveals successive steps leading to miRNA‐mediated silencing in mammalian cells

“…In future, it will be important to identify signals in the mRNA 3 0 UTRs and factors that may regulate transition from one silencing stage to another, and thus control the final outcome of miRNA-mediated repression of different mRNAs. During revision of our manuscript, two papers reported that also in zebrafish and Drosophila S2 cells, translational repression precedes mRNA deadenylation and decay [29,30].…”

YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA

“…For the comparison of PAR-CLIP and m 6 A peaks, at least 1 bp overlap was applied as the criteria of overlap peaks. Nonparametric Mann-Whitney U-test (Wilcoxon rank-sum test, two sided, significance level = 0.05) was applied in ribosome profiling data analysis as previous reported [48]. GO term analyses were performed by DAVID [49,50].…”

Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation

“…Ribosome profiling or Ribo-seq, based on deep sequencing of ribosome-protected mRNA fragments (RPFs), has proven to be powerful in determining ribosome positions and densities across the entire transcriptome [11]. Many research groups have successfully applied Ribo-seq to a wide range of organismal species and reported pervasive pause sites along the coding region (CDS) of mRNAs [12][13][14][15][16][17][18]. From bacteria to human cells, the most consistent pause npg www.cell-research.com | Cell Research sites are located at the start and stop codons, which is in line with the notion that ribosomes tend to pause during initiation and termination [10].…”