The dark proteome: translation from noncanonical open reading frames

Omics-based technologies have revolutionized our understanding of the coding potential of the genome. In particular, these studies revealed widespread unannotated open reading frames (ORFs) throughout genomes and that these regions have the potential to encode novel functional (micro-)proteins and/or hold regulatory roles. However, despite their genomic prevalence, relatively few of these noncanonical ORFs have been functionally characterized, likely in part due to their under-recognition by the broader scientific community. The few that have been investigated in detail have demonstrated their essentiality in critical and divergent biological processes. As such, here we aim to discuss recent advances in understanding the diversity of noncanonical ORFs and their roles, as well as detail biologically important examples within the context of the mammalian genome. Mounting evidence of widespread noncanonical translation suggests that the protein-coding potential of the human genome has been underestimated.Recent advances in techniques to probe the translatome and proteome have highlighted noncanonical open reading frames (ORFs) that (i) govern translational regulation, (ii) produce functional microproteins, and/or (iii) encode protein variants of the canonical coding sequence.There are accumulating examples within the literature of noncanonical ORF-encoded proteins that possess important functional and physiological roles, but there lie thousands of putative ORFs within ‘omics’ databases that are left unverified and functionally uncharacterized.