Visualization of Exon Junction Complex (EJC) and related factors at transcription sites of Drosophila polytene chromosomes

It was long believed that cytoplasmic events like translation and mRNA degradation are not linked to nuclear events such as pre-mRNA splicing. However, current observation indicates that nucleus/cytoplasm communication is mediated by the exon junction complex (EJC), a multiprotein complex deposited during splicing in the nucleus. The consensus is that the EJC is deposited exclusively on spliced mRNA, 20-24 nucleotides upstream of the exon-exon junction. Splicing appears to deposit the EJC similarly in \(Drosophila\) \(melanogaster\), yet it has also been reported that, in contrast to mammalian cells, the EJC might be required for splicing, suggestive an earlier association with pre-mRNA. My PhD project aimed to visualize the assembly of the EJC on nascent RNA at polytene chromosome transcription sites. The main conclusion of these studies is that, contrary to current predictions, EJC components are recruited at transcription sites corresponding to both intron-containing and intron-less genes. A similar conclusion was reached in \(Drosophila\) S2 cells, where chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) data indicates, the core EJC protein Y14 associates to transcription sites independently of the gene having introns. Additionally, in a parallel projects my data also suggest that ribosomal proteins and UPF1 also associate with Pol II transcription sites