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

Wen Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei Kosakovsky Pond, Anton Nekrutenko

Research output: Contribution to journalArticle

43 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)855-861
Number of pages7
JournalPLoS Computational Biology
Volume3
Issue number5
DOIs
StatePublished - May 1 2007

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Reading Frames
Genome
genome
Coding
Genes
Gene
Proteins
protein
gene
Overlapping
Mammals
genes
codons
Codon
Artifacts
Open Reading Frames
artifact
open reading frames
mammal
proteins

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Cite this

Chung, Wen Yu ; Wadhawan, Samir ; Szklarczyk, Radek ; Pond, Sergei Kosakovsky ; Nekrutenko, Anton. / A first look at ARFome : Dual-coding genes in mammalian genomes. In: PLoS Computational Biology. 2007 ; Vol. 3, No. 5. pp. 855-861.
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A first look at ARFome : Dual-coding genes in mammalian genomes. / Chung, Wen Yu; Wadhawan, Samir; Szklarczyk, Radek; Pond, Sergei Kosakovsky; Nekrutenko, Anton.

In: PLoS Computational Biology, Vol. 3, No. 5, 01.05.2007, p. 855-861.

Research output: Contribution to journalArticle

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