ArticlePloS one2018
Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 66 citations in OpenAlex.
- Pooled it
- Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes.Journal of molecular evolution · 2026Article
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- Highly Virulent Newcastle Disease Virus in Eurasian Collared Doves in the North of Portugal.Animals : an open access journal from MDPI · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Splam: a deep-learning-based splice site predictor that improves spliced alignments.Genome biology · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene.Viruses · 2024Article
- Exposing the small protein load of bacterial life.FEMS microbiology reviews · 2023Review
- Splam: a deep-learning-based splice site predictor that improves spliced alignments.bioRxiv : the preprint server for biology · 2023Article
- Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities.Genomics, proteomics & bioinformatics · 2023Article
- A novel ambigrammatic mycovirus, PsV5, works hand in glove with wheat stripe rust fungus to facilitate infection.Plant communications · 2023Article
- Structural analysis and molecular dynamics simulation studies of HIV-1 antisense protein predict its potential role in HIV replication and pathogenesis.Frontiers in microbiology · 2023Article
- Analysis of nested alternate open reading frames and their encoded proteins.NAR genomics and bioinformatics · 2022Article
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications.Current opinion in virology · 2022Review
- Using networks to analyze and visualize the distribution of overlapping genes in virus genomes.PLoS pathogens · 2022Article
- Article
- Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting.Frontiers in molecular biosciences · 2022Review
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 6 institutions in 4 countries.
Funding
Abstract
Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a high-quality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.