Dowling D, Schmitz JF, Bornberg-Bauer E
Nascent de novo genes may be conserved for millions of years in humans and other primates
Molecular Biology & Evolution, 2019

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Abstract

Novel genes, including de novo genes, are thought to play an important role in the evolution of lineage-specific traits and adaptations. De novo genes arise from ancestrally non-coding DNA and have been identified in a broad range of taxonomic groups including animals, fungi, and plants. However, it remains unclear how these genes evolve structural properties that enable them to become integrated into pre-existing cellular networks.
Here we use transcriptomics data to identify recently emerged open reading frames (ORFs) in human and five other primates. We identify novel human-specific ORFs, in addition to conserved ORFs between human and the investigated primate species. Moreover, we find that novel ORFs are significantly shorter than old ORFs. We show that the majority of the conserved ORFs between primates are under purifying selection, which suggests that they code for functional peptides. We predict structural properties, such as intrinsic disorder and aggregation propensity. We find that novel ORFs are not structurally uniform, but rather structurally diverse - as are old ORFs. This suggests that there is no process of structural maturation, aside from slight increases in sequence length. These data support a model in which de novo gene emergence produces a population of structurally varied micro-peptides, some of which may acquire functional roles by chance and remain conserved over millions of years.