Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias. Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias

To characterize the rules governing exon recognition during splicing, we analyzed RNA-seq datasets and identified ~4,000 GC-rich and ~5,000 AT-rich exons, labelled GC-exons and AT-exons, respectively whose inclusion depends on different sets of splicing factors. We show that a high GC-load is associated with predicted RNA secondary structures at 5'ss and that GC-exons are dependent on U1 snRNP-associated proteins. Meanwhile, a high AT-load is associated with a large number of decoy splicing-related signals upstream exons such as the number of branchpoints and SF1- or U2AF65-binding sites and AT-exons are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization. Since the GC content of exons correlates with that of their hosting-genes, -isochores and – topologically-associated domains, we propose that regional nucleotide composition bias leaves a footprint locally, at the exon level, inducing, during splicing, constraints that are alleviated by the local chromatin organization and specific splicing factors. Overall design: Samples siFUS, siGL2, siHNRNPC, siHNRNPH1, siHNRNPK and siTRA2A-B were made together and are part of the same experiment (simplicates). Samples siPP-1, siPP-2, siPP-3, siGL2-1, siGL2-2 and siGL2-3 were made together from different cell batchs and are part of the same experiment (triplicates).