ArticleJournal of molecular evolution2011
Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences.
Article in Journal of molecular evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- Ambisense polarity of genome RNA of orthomyxoviruses and coronaviruses.World journal of virology · 2021Review
- Unique Bipolar Gene Architecture in the RNA Genome of Influenza A Virus.Biochemistry. Biokhimiia · 2020Article
- NSP Protein Encoded in Negative NS RNA Strand of Influenza A Virus Induces Cellular Immune Response in Infected Animals.Doklady. Biochemistry and biophysics · 2019Article
- A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.Molecular biology and evolution · 2018Article
- Influenza A Virus Negative Strand RNA Is Translated for CD8Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- Evolution of Therapeutic Antibodies, Influenza Virus Biology, Influenza, and Influenza Immunotherapy.BioMed research international · 2018Review
- Negative-sense virion RNA of segment 8 (NS) of influenza a virus is able to translate in vitro a new viral protein.Doklady. Biochemistry and biophysics · 2017Article
- Compounds with anti-influenza activity: present and future of strategies for the optimal treatment and management of influenza. Part I: Influenza life-cycle and currently available drugs.Journal of preventive medicine and hygiene · 2014Review
- Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry.PLoS pathogens · 2012Article
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
Abstract
Protein-coding genes often contain long overlapping open-reading frames (ORFs), which may or may not be functional. Current methods that utilize the signature of purifying selection to detect functional overlapping genes are limited to the analysis of sequences from divergent species, thus rendering them inapplicable to genes found only in closely related sequences. Here, we present a method for the detection of selection signatures on overlapping reading frames by using closely related sequences, and apply the method to several known overlapping genes, and to an overlapping ORF on the negative strand of segment 8 of influenza A virus (NEG8), for which the suggestion has been made that it is functional. We find no evidence that NEG8 is under selection, suggesting that the intact reading frame might be non-functional, although we cannot fully exclude the possibility that the method is not sensitive enough to detect the signature of selection acting on this gene. We present the limitations of the method using known overlapping genes and suggest several approaches to improve it in future studies. Finally, we examine alternative explanations for the sequence conservation of NEG8 in the absence of selection. We show that overlap type and genomic context affect the conservation of intact overlapping ORFs and should therefore be considered in any attempt of estimating the signature of selection in overlapping genes.
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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.