Translational landscape during seed germination revealed by ribosome profiling.

Seed germination is crucial for agricultural reproduction. A deep understanding of this process can secure healthy growth at the early phases of plant development and therefore yield. Recent research indicates that germination is a complex process involving translational regulation. A large group of seed-stored mRNAs together with newly synthesized transcripts are regulated by post-transcriptional mechanisms and selectively translated at different stages to support the germination process. To investigate the mechanism of translational control, we performed ribosome profiling on mRNAs of distinct physiological stages during Arabidopsis thaliana seed germination. The presence of ribosome association on mRNAs with three-nucleotide periodicity indicates their capacity for translation. Dry seeds, in which translation is on hold, are characterized by a unique ribosome association landscape with a higher ribosome association at the 5' and 3' UTR, compared with physiological stages that show active translation. Start codon-specific stalling of ribosomes in dry seeds is associated with an adenine-enriched sequence motif. Throughout germination, codons encoding glycine, aspartate, tyrosine, and proline are the most frequent ribosome pausing sites. Moreover, the non-coding ribosome-associated RNAs that we identified are indeed translated, as was revealed by investigating total seed proteome data. Seed-specific upstream open reading frames (uORFs) have been identified that may play a role in translational regulation of early seed germination. Altogether, we present a first ribosome profiling analysis across seed germination that illuminates various regulatory mechanisms that potentially contribute to the seed's survival strategy.