title: Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.
abstract: A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this goal proved challenging because of the large proportion of the mouse and human genomes that is apparently conserved but apparently does not code for protein. We developed a two-stage procedure that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods. RT-PCR amplification and direct sequencing applied to an initial sample of mouse predictions that do not overlap previously known genes verified the regions flanking one intron in 139 predictions, with verification rates reaching 76%. On average, the confirmed predictions show more restricted expression patterns than the mouse orthologs of known human genes, and two-thirds lack homologs in fish genomes, demonstrating the sensitivity of this dual-genome approach to hard-to-find genes. We verified 112 previously unknown homologs of known proteins, including two homeobox proteins relevant to developmental biology, an aquaporin, and a homolog of dystrophin. We estimate that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes. This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes.
authors.affiliation: Research Group in Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra/Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigo
authors.forename: Emmanouil T
authors.initials: ET
authors.lastname: Dermitzakis
authors.forename: Pankaj
authors.initials: P
authors.lastname: Agarwal
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Genis
authors.initials: G
authors.lastname: Parra
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.forename: Josep F
authors.initials: JF
authors.lastname: Abril
authors.forename: Evan
authors.initials: E
authors.lastname: Keibler
authors.forename: Robert
authors.initials: R
authors.lastname: Lyle
authors.forename: Catherine
authors.initials: C
authors.lastname: Ucla
authors.forename: Stylianos E
authors.initials: SE
authors.lastname: Antonarakis
authors.forename: Michael R
authors.initials: MR
authors.lastname: Brent
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005091:Exons; D005821:Genetic Techniques; D016678:Genome; D015894:Genome, Human; D006801:Humans; D007438:Introns; D051379:Mice; D008969:Molecular Sequence Data; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014018:Tissue Distribution