Interplay between coding and exonic splicing regulatory sequences

Abstract

The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any splicing factor share a similar nucleotide composition bias. We next demonstrate that coregulated exons preferentially code for amino acids with similar physicochemical properties because of the non-randomness properties of the genetic code. Indeed, amino acids sharing physicochemical properties correspond to codons that have the same nucleotide composition bias. These observations reveal an unanticipated bidirectional interplay between the physicochemical features encoded by exons and exon splicing regulation by splicing factors. We propose that the splicing regulation of an exon by a splicing factor is tightly interconnected with the physicochemical properties of the exon-encoded protein domain depending on the splicing-factor affinity for specific nucleotides.