Abstract Most protein-coding genes in humans and other eukaryotes are made up of a collection of exons, which are concatenated to form the messenger RNA (mRNA) that encodes a final protein product. The well-known phenomenon of alternative splicing makes it possible for a single gene to encode multiple protein products, by conditionally including only a subset of the gene’s exons into the expressed mRNA. A more surprising mechanism for producing alternate protein products is to utilize an alternate reading frame of a standard exon, through aberrant splicing; using custom software built in our research group, we have found that this mechanism appears to be quite common. Specifically, ~13% of all human genes include at least one exon that conditionally encodes alternate peptides, and these “dual-coding exons” are highly-conserved: 98% correspond to homologous exons in the mouse genome that also encode two open reading frames. Light exploration has identified dozens of human genes that show tissue-specific patterns of reading frame usage, suggesting a functional role for at least some of these variants. Here, we describe a plan to (i) leverage massive public atlases of human tissue-specific and development-specific RNA-Seq and mass spectrometry data to tabulate the extent of differential use of these frame-shifted splicing variants, and to (ii) analyze the computationally-predicted structural and functional impact of dual-coding variants, and the sequence signals controlling them. The results of these analyses will be accumulated for release in an open and accessible web service.

Narrative We have found that ~13% of all human genes include at least one exon that can (and apparently does) encode two distinct peptides, depending on condition-specific splicing activity. These surprisingly prevalent human dual-coding exons nearly all show similar dual-coding nature in the mouse genome – this extent of conservation strongly suggests that they play an important biological role. Here, we describe a plan to catalog the tissue- and development-specific splicing patterns of dual-coding variants, and to computationally explore their mechanisms of control and expected functional impact. This work will establish a robust repository of analysis of this exciting and poorly understood mode of controlling gene function and activity, and will lay the groundwork for its future study.