title: 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.
authors.affiliation: Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
authors.forename: Wen-Yu
authors.initials: WY
authors.lastname: Chung
authors.forename: Samir
authors.initials: S
authors.lastname: Wadhawan
authors.forename: Radek
authors.initials: R
authors.lastname: Szklarczyk
authors.forename: Sergei Kosakovsky
authors.initials: SK
authors.lastname: Pond
authors.forename: Anton
authors.initials: A
authors.lastname: Nekrutenko
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D008322:Mammals / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D022821:RNA Splice Sites