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A first look at ARFome: dual-coding genes in mammalian genomes.

ABSTRACT: Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes. Indeed, codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints, making it a costly arrangement. Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions. Using newly developed statistical techniques, we identified 40 candidate genes with evolutionarily conserved overlapping coding regions. Because our approach is conservative, we expect mammals to possess more dual-coding genes. Our results emphasize that the skepticism surrounding eukaryotic dual coding is unwarranted: rather than being artifacts, overlapping reading frames are often hallmarks of fascinating biology.

SUBMITTER: Chung WY

PROVIDER: S-EPMC1868773 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature

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A first look at ARFome: dual-coding genes in mammalian genomes.

Chung Wen-Yu WY Wadhawan Samir S Szklarczyk Radek R Pond Sergei Kosakovsky SK Nekrutenko Anton A

PLoS computational biology 20070501 5

Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes. Indeed, codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints, making it a costly arrangement. Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions ...[more]

PMID: 17511511

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