ArticlePLoS genetics2015
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Review
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Phylostratigraphic Analysis Reveals the Evolutionary Origins and Potential Role of New Genes in the Adaptive Evolution ofInternational journal of molecular sciences · 2026Article
- Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- Improved sampling of genotypes and species reveals new insights on de novo gene history and regulatory origins.Genetics · 2025Article
- The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported.Journal of molecular evolution · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 2024Article
- De Novo Genes.Annual review of genetics · 2024Review
- Reply to: Identification of old coding regions disproves the hominoid de novo status of genes.Nature ecology & evolution · 2024Article
- Identification of old coding regions disproves the hominoid de novo status of genes.Nature ecology & evolution · 2024Article
- Noncanonical microprotein regulation of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Review
- Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome.Genome biology · 2024Article
- High Polymorphism Levels of De Novo ORFs in a Yoruba Human Population.Genome biology and evolution · 2024Article
- A Synergistic, Cultivator Model of De Novo Gene Origination.Genome biology and evolution · 2024Article
- Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.
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