De novo birth of functional, human-specific microproteins

Abstract

We now have a growing understanding that functional short proteins can be translated out of small Open Reading Frames (sORF). Such ″microproteins″ can perform crucial biological tasks and can have considerable phenotypic consequences. However, their size makes them less amenable to genomic analysis, and their evolutionary origins and conservation are poorly understood. Given their short length it is plausible that some of these functional microproteins have recently originated entirely de novo from non-coding sequence. Here we test the possibility that de novo gene birth can produce microproteins that are functional ″out-of-the-box″. We reconstructed the evolutionary origins of human microproteins previously found to have measurable, statistically significant fitness effects. By tracing the appearance of each ORF and its transcriptional activation, we were able to show that, indeed, novel small proteins with significant phenotypic effects have emerged de novo throughout animal evolution, including many after the human-chimpanzee split. We show that traditional methods for assessing the coding potential of such sequences often fall short, due to the high variability present in the alignments and the absence of telltale evolutionary signatures that are not yet measurable. Thus we provide evidence that the functional potential intrinsic to sORFs can be rapidly, and frequently realised through de novo gene birth.

Accurate identification of de novo genes in plant genomes using machine learning algorithms

“…To this end, we applied a minimum threshold of 30% coverage between A. thaliana DNGs and Brassicaceae genomes as corresponding to conserved synteny. This length threshold is lower than those used in previous DNG analyses in animals (31, 85, 86), in order to account for the decreased overall synteny conservation among Brassicaceae. Furthermore, the syntenic alignments were screened for the presence of enabler substitutions, represented by a novel start codon, the removal of stop codons and/or frameshifts in the DNG coding region compared to the syntenic DNA of the outgroup species.…”

Origin of functional de novo genes in humans from “hopeful monsters”

“…Moreover, the annotations of additional novel ORFs through the deep integration of these data are certainly needed in future investigations. For example, owing to the high sensitivity of ribosome profiling data, many regions previously defined as noncoding have been revealed to seemingly encode novel microproteins (Vakirlis et al, 2021). It is thus interesting to investigate whether these signals indeed represent bona fide translation of new proteins in vivo and whether any polycistronic regulation is involved in determining which ORF to translate for a specific transcript with multiple newly annotated ORFs.…”

“…Y. Chen et al, 2015;Knowles & McLysaght, 2009;C. Y. Li et al, 2010;Ruiz-Orera et al, 2015;Vakirlis et al, 2021;D. D. Wu et al, 2011;Xie et al, 2012).…”

“…Taken together, although there is a consensus for the definition of de novo genes in the field, the list of de novo genes in humans has expanded with the introduction of new genomic technologies. Starting from the initial reports of three human‐specific de novo genes ( CLLU1 , C22orf45 , and DNAH10OS ) by Knowles and McLysaght (2009) and C20orf203 by C. Y. Li et al (2010), dozens of human‐ or hominoid‐specific de novo genes have since been reported, with new genomic technologies such as transcriptome sequencing and ribosome profiling providing evidence of the expression of these new genes (An et al, 2023; J. Y. Chen et al, 2015; Knowles & McLysaght, 2009; C. Y. Li et al, 2010; Ruiz‐Orera et al, 2015; Y. Shao et al, 2019; Vakirlis et al, 2021; D. D. Wu et al, 2011; Xie et al, 2012). According to a recent review by Luuk et al, 82 de novo genes originated recently in the human lineage during the primate evolution (Broeils et al, 2023).…”