Overlapping gene
An overlapping gene is a gene whose expressible nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene.[1] In this way, a nucleotide sequence may make a contribution to the function of one or more gene products.
Different types of overlap
Tandem out-of-phase overlap of the human mitochondrial genes ATP8 (+1 frame, in red) and ATP6 (+3 frame, in blue)[2]
Two different kinds of gene overlap are found in the genomes.[3]
- Tandem overlap: the shared nucleotide sequence of the two overlapping genes may be read in identical or alternate reading frames during translation. When the shared sequences use the same reading frame, the overlap is in-phase. When they use different reading frames, the overlap is out-of-phase.[4] The tandem overlap can be written as ⇒⇒ where arrows symbolize the reading frame from start to end.
- Antiparallel strands overlap: in double-stranded DNA, overlapping genes also occur on opposite strands. Part of the antisense strand of one gene may form part of the sense strand of a different gene. There are two possibilities of antiparallel overlap.
- The start-on overlap occurs when reading frames on opposite strands overlap on their beginning. This can be written as ⇐⇒.
- The end-on overlap occurs when reading frames on opposite strands overlap on their end. This can be written as ⇒⇐.
A survey of ca. 65,000 gene overlaps in microbial genomes showed that 4.1%, 6.2% and 6.0% respectively occurred in-phase, and with a +1 or +2 out-of-phase shift for antiparallel overlaps (⇒⇐ and ⇐⇒), whereas 0.1% (in-phase), 25.9% (+1 frameshift) and 57.8% (+2 frameshift) were recorded for tandem overlaps.[3]
Occurrence in various organisms
Overlapping genes in the bacteriophage ΦX174 genome. There are 11 genes in this genome (A, A*, B-H, J, K). Genes B, K, E overlap with genes A, C, D.
Overlapping genes have been found in multiple domains of life.
- Bacteria: studies have found that up to one third of the bacterial genomes participates in gene overlap.[5]
- Viruses: the first DNA genome ever sequenced — the one of bacteriophage ΦX174 — revealed several occurrences of overlapping reading frames.[6]
- Eukaryotes: examples are documented in mammals, including human and mouse.[7]
References
- ↑ Y. Fukuda, M. Tomita et T. Washio (1999). "Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae". Nucl. Acids Res. (Oxford Journals) 27 (8): 1847–1853. doi:10.1093/nar/27.8.1847.
- ↑ Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (Apr 1981). "Sequence and organization of the human mitochondrial genome". Nature 290 (5806): 457–465. doi:10.1038/290457a0. PMID 7219534.
- 1 2 Johnson Z, Chisholm S (2004). "Properties of overlapping genes are conserved across microbial genomes". Genome Res 14 (11): 2268–72. doi:10.1101/gr.2433104. PMC 525685. PMID 15520290.
- ↑ Normark S., Bergstrom S., Edlund T., Grundstrom T., Jaurin B., Lindberg F.P., Olsson O. (1983). "Overlapping genes". Annual Review of Genetics 17: 499–525. doi:10.1146/annurev.ge.17.120183.002435. PMID 6198955.
- ↑ Huvet, Maxime; Stumpf, Michael (2014). Overlapping genes; a window on gene evolution. BioMed Central Ltd.
- ↑ Sanger, F.; Air, G. M.; Barrell, B. G.; Brown, N. L.; Coulson, A. R.; Fiddes, J. C.; Hutchison, C. A.; Slocombe, P. M.; Smith, M. (1977). "Nucleotide sequence of bacteriophage ΦX174 DNA". Nature 265 (5596): 687–95. Bibcode:1977Natur.265..687S. doi:10.1038/265687a0. PMID 870828.
- ↑ C. Sanna, W. Li et L. Zhang (2008). "Overlapping genes in the human and mouse genomes". BMC Genomics 9 (169). doi:10.1186/1471-2164-9-169.
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