XB-ART-48919Nature. April 3, 2014; 508 (7494): 66-71.
Poly(A)-tail profiling reveals an embryonic switch in translational control.
Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other ''housekeeping'' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA-mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.
PubMed ID: 24476825
PMC ID: PMC4086860
Article link: Nature.
Grant support: GM067031 NIGMS NIH HHS , R01 GM067031 NIGMS NIH HHS , T32 GM007753 NIGMS NIH HHS , T32GM007753 NIGMS NIH HHS , Howard Hughes Medical Institute
Genes referenced: ddx24 pam tes
Article Images: [+] show captions
|Figure 3. Transient coupling between poly(A)-tail length and TEa, Relationship between mean tail length and TE for genes with ≥50 poly(A) tags from embryonic samples at the indicated developmental stages. For each stage, tail lengths and TEs were obtained from the same sample. MGC116473 and DDX24 fell outside the plot for X. laevis, stages 3–4, and LOC100049092 fell outside the plot for X. laevis, stages 12–12.5. b, Relationship between mean tail length and TE in the indicated cells, for genes with ≥50 (yeasts) or ≥100 (others) tags. With the exception of HeLa35, tail lengths and TEs were from the same samples. Budding yeast YBR196C, YLR355C and YDL080C, fission yeast SPCC63.04.1, mouse-liver NM_007881 and NM_145470, HEK293T NM_001007026, NM_021058, and NM_003537 and HeLa NM_001007026 fell outside their respective plots.|
|Figure 4. No detectable intragenic coupling between poly(A)-tail length and TEa, Global analysis of tail lengths across the polysome profile for 3T3 cells. UV absorbance indicates mean number of ribosomes bound per mRNA for each fraction from the sucrose gradient (top, fractions demarcated with vertical dashed lines). Boxplots show distributions of tail lengths in each fraction for all tags mapping to annotated 3′ UTRs (bottom). Boxplot percentiles are line, median; box, 25th and 75th percentiles; whiskers, 10th and 90th percentiles. The horizontal line indicates the overall median of the median tail lengths. b, Relationship between tail lengths and ribosomes bound per mRNA for mRNAs from the same gene. For each gene, the data from a were used to plot the mean tail length as a function of bound ribosomes. Log-log plots for 8 randomly selected genes with ≥50 poly(A) tags in ≥6 fractions are shown (left), with lines indicating linear least-squared fits to the data (adding a pseudocount of 0.5 ribosomes to the fraction with 0 ribosomes). The boxplot shows the distribution of slopes for all genes with ≥50 poly(A) tags in ≥4 fractions (right; n = 4,079; one-sided, one-sample Wilcoxon test; boxplot percentiles as in a).|