Translational landscape during Seed Germination at Sub-Codon resolution

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 the 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 3-nucleotide periodicity of the ribosome association on mRNAs identified indicates their translational potential. Dry seeds, in which translation is on hold are characterized by a unique ribosome association landscape with high association at the 5 and 3 UTR, compared to 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 RNAs which we identified as associated to ribosomes are indeed translated as was revealed by investigating total seed proteome data. Seed specific upstream Open Reading Frames (uORFs) are identified which may be associated to translational control of adaptative response during early seed germination. Altogether, we present a first ribosome profiling analysis across seed germination that illuminates various regulatory mechanisms that potentially contribute to the seeds survival strategy.