Transcriptome-wide binding sites of mutually exclusive exon junction complexes

The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. In this study we show that EJC exists in two mutually exclusive compositions characterized by peripheral proteins RNPS1 and CASC3. We identified transcriptome-wide binding sites of the two alternate EJCs via RNA:protein immunoprecipitation in tandem followed by deep sequencing (RIPiT-Seq). We show that RNPS1-EJC, which is an SR-rich mega-dalton sized RNP, is the major EJC form in the nucleus. After mRNP export to the cytoplasm and before translation, the EJC undergoes a remarkable compositional and structural remodeling into an SR- and RNPS1-devoid monomeric complex that contains CASC3. The CASC3-EJC is enriched on cytoplasmic RNAs and is the main EJC form that encounters ribosome and undergoes disassembly during translation. Analysis of exon junction complex footprints using RIPiT-Seq