Overlapping gene

An overlapping gene is a gene whose expressible nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene. In this way, a nucleotide sequence may make a contribution to the function of one or more gene products. Overprinting refers to a type of overlap in which all or part of the sequence of one gene is read in an alternate reading frame from another gene at the same locus. Overprinting has been hypothesized as a mechanism for de novo emergence of new genes from existing sequences, either older genes or previously non-coding regions of the genome. Overprinted genes are particularly common features of the genomic organization of viruses, likely to greatly increase the number of potential expressible genes from a small set of viral genetic information.

Genes may overlap in a variety of ways and can be classified by their positions relative to each other.

Overlapping genes can also be classified by phases, which describe their relative reading frames:

Overlapping genes are particularly common in rapidly evolving genomes, such as those of viruses, bacteria, and . They may originate in three ways:

The use of the same nucleotide sequence to encode multiple genes may provide evolutionary advantage due to reduction in genome size and due to the opportunity for transcriptional and translational co-regulation of the overlapping genes. Gene overlaps introduce novel evolutionary constraints on the sequences of the overlap regions.

Certain types of gene overlap provide evidence that one of the genes in the pair may have originated de novo, rather than from gene duplication or other mechanisms by which new genes are created. In 1977, Pierre-Paul Grassé proposed the possibility that genes could be generated de novo by mutations in existing genetic sequences to introduce novel ORFs in alternate reading frames; he described the mechanism as overprinting. It was later substantiated by Susumu Ohno, who identified a candidate gene that may have arisen by this mechanism. The mechanism is equally applicable both to generation of a novel ORF overlapping an existing one, and to generation of a novel ORF from previously non-coding DNA. It has since been proposed as a common source of de novo genes, which may make up a significant fraction of so-called "ORFan" or taxonomically restricted genes.

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