Final Report Summary - SPLICING IN MITOSIS (Regulation of cell division by alternative splicing) The main objective of this proposal was to investigate the role of alternative splicing (AS) - the process by which multiple, distinct transcript and protein variants are expressed from a single gene - in regulating cell division and mitosis. The primary aim of this project was to identify whether alternative splicing plays a role in regulating the cell cycle. Importantly, therefore, the first major finding of this project is that approximately 1,300 genes have cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose protein levels undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control. The second major aim of this project was to assess the impact of alternative splicing on proteome diversity and regulation. Notably, this project identified that at least 75% of human exon skipping events detected in medium to high abundance transcripts using RNA-Seq data are also detected by ribosome profiling data. We further identified that relatively small subsets of functionally related splice variants are engaged by ribosomes at levels that do not reflect their absolute abundance, indicating an important role for AS in modulating translational output. This mode of regulation is associated with the control of the mammalian cell cycle. These results suggest that a major fraction of splice variants is translated, and that specific cellular functions including cell cycle control are subject to AS-dependent modulation of translation output.A third major goal of this project was to investigate the role of alternative splicing in cancer. We were able to identify a significant increase in splicing complexity in cancer tissues compared to control tissues, and that these differences correlate with increased expression of proto-oncogenic splicing factors. This work provides further evidence of alternative splicing mis-regulation being a major hallmark of cancer.This project successfully integrated and processed large-scale biological data to produce novel biological insights, as demonstrated by multiple high-impact publications. Furthermore, this project opened up a novel avenue for cancer research by identifying alternative splicing as a widespread mechanism controlling cell division. This project has therefore successfully addressed two major priorities of the 7th Framework Programme (integration of big data and impacting cancer research).
