ArticleBMC genomics2008
Non-random retention of protein-coding overlapping genes in Metazoa.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Enigmatic Nodal and Lefty gene repertoire discrepancy: Latent evolutionary history revealed by vertebrate-wide phylogeny.Developmental dynamics : an official publication of the American Association of Anatomists · 2025Review
- Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).G3 (Bethesda, Md.) · 2024Article
- Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair.Journal of molecular evolution · 2023Article
- azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion.PLoS biology · 2023Article
- The Roles of Antisense Long Noncoding RNAs in Tumorigenesis and Development through Cis-Regulation of Neighbouring Genes.Biomolecules · 2023Review
- The Functional Meaning of 5'UTR in Protein-Coding Genes.International journal of molecular sciences · 2023Review
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes.BMC genomics · 2021Article
- The Diverse Roles of TIMP-3: Insights into Degenerative Diseases of the Senescent Retina and Brain.Cells · 2019Review
- Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana.Scientific reports · 2017Article
- Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa.BMC genomics · 2017Article
- Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.BMC genomics · 2016Article
- Neighboring gene regulation by antisense long non-coding RNAs.International journal of molecular sciences · 2015Review
- Overlapping genes of Aedes aegypti: evolutionary implications from comparison with orthologs of Anopheles gambiae and other insects.BMC evolutionary biology · 2013Article
- Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis.Plant physiology · 2013Article
- Mechanisms and dynamics of orphan gene emergence in insect genomes.Genome biology and evolution · 2013Article
- Pathogenetic model for Tourette syndrome delineates overlap with related neurodevelopmental disorders including Autism.Translational psychiatry · 2012Review
- Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals.Human genetics · 2012Article
- Profiles of small non-coding RNAs in Schistosoma japonicum during development.PLoS neglected tropical diseases · 2011Article
- Alpha T-catenin (CTNNA3): a gene in the hand is worth two in the nest.Cellular and molecular life sciences : CMLS · 2011Review
Corrections and comments
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Authors and funding
9 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm).
resultsFor all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression.
conclusionOur data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.
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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.