Multilayered control of alternative splicing regulatory networks by transcription factors (iCLIP-Seq). Mus musculus

Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms. Overall design: iCLIP-seq of Nacc1 (2 replicates and input) and Flag-Zfp871 (2 replicates of 2 clones each) in N2A cells ------------------------------------------ Authors state that the 'processed data' consist of a plot only since the analyses (including the plots as supplementary files) were done directly from raw data.