For birth of a de novo protein-coding gene to occur, a non-genic sequence must both be transcribed and acquire an ORF before becoming translated. These events could occur in either order, and there is evidence supporting both an “ORF first” and a “transcription first” model. An analysis of de novo genes that are segregating in D. melanogaster found that sequences that are transcribed had similar coding potential to the orthologous sequences from lines lacking evidence of transcription. This finding supports the notion that many ORFs can exist prior to being transcribed. The antifreeze glycoprotein gene AFGP, which emerged de novo in Arctic codfishes, provides a more definitive example in which the de novo emergence of the ORF was shown to precede the promoter region. Furthermore, putatively non-genic ORFs long enough to encode functional peptides are numerous in eukaryotic genomes, and expected to occur at high frequency by chance. Through tracing the evolution history of ORF sequences and transcription activation of human de novo genes, a study showed that some ORFs were ready to confer biological significance upon their birth. At the same time, transcription of eukaryotic genomes is far more extensive than previously thought, and there are documented examples of genomic regions that were transcribed prior to the appearance of an ORF that became a de novo gene. The proportion of de novo genes that are protein-coding is unknown, but the appearance of “transcription first” has led some to posit that protein-coding de novo genes may first exist as RNA gene intermediates. The case of bifunctional RNAs, which are both translated and function as RNA genes, shows that such a mechanism is plausible.
