Analysis of post-transcriptional regulation during early Drosophila development by ribosome profiling

Abstract

Post-transcriptional regulation is a critical mechanism for controlling protein expression in many cellular contexts. During early Drosophila development, post-transcriptional regulation is especially important as the expression of proteins encoded by maternally provided mRNAs must be spatially and temporally regulated within a single cell. Translational control is one mechanism by which this is accomplished and the translational regulation of specific transcripts that are involved in development has been the subject of much study. Recent advances in high-throughput sequencing now allow genome-wide analysis of translation by ribosome profiling, which maps the position of ribosomes along all transcripts in the genome. Using this technique, we have measured ribosome occupancy during Drosophila development for all transcripts in the genome.

Translation of transcripts involved in RNA transport and regulation was found to be significantly enriched in total ovary samples compared to early embryos by Gene Set Enrichment Analysis (GSEA). We also developed a method to scan through the ribosome profiles of all transcripts in the genome, finding several instances of asymmetric ribosome distribution that might be indicative of translational regulatory events.

Finally, we investigated the ribosome coverage of the nanos (nos) transcript, a maternally provided mRNA whose translational regulation is critical for early embryonic development. Ribosome coverage of nos in ovary and early embryo samples is consistent with its translational state during development and the distribution of ribosomes is also dynamic during development. However, the data contradict a previously proposed model for translational repression of nos at a post-initiation step. The acquisition of data from experiments completed with ovary tissue will allow the completion of further computational analyses to characterize the translational phenomena observed in Drosophila ovaries and early embryos.