title: A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells.
abstract: Embryonic stem (ES) cells are pluripotent cell lines with the capacity of self-renewal and the ability to differentiate into specific cell types. We performed the first genome-wide analysis of the mouse ES cell transcriptome using approximately 250,000 gene trap sequence tags deposited in public databases. We unveiled >8000 novel transcripts, mostly non-coding, and >1000 novel alternative and often tissue-specific exons of known genes. Experimental verification of the expression of these genes and exons by RT-PCR yielded a 70% validation rate. A novel non-coding transcript within the set studied showed a highly specific pattern of expression by in situ hybridization. Our analysis also shows that the genome presents gene trapping hotspots, which correspond to 383 known and 87 novel genes. These "hypertrapped" genes show minimal overlap with previously published expression profiles of ES cells; however, we prove by real-time PCR that they are highly expressed in this cell type, thus potentially contributing to the phenotype of ES cells. Although gene trapping was initially devised as an insertional mutagenesis technique, our study demonstrates its impact on the discovery of a substantial and unprecedented portion of the transcriptome.
authors.affiliation: Telethon Institute of Genetics and Medicine, 80131 Napoli, Italy.
authors.forename: Guglielmo
authors.initials: G
authors.lastname: Roma
authors.forename: Gilda
authors.initials: G
authors.lastname: Cobellis
authors.forename: Pamela
authors.initials: P
authors.lastname: Claudiani
authors.forename: Francesco
authors.initials: F
authors.lastname: Maione
authors.forename: Pedro
authors.initials: P
authors.lastname: Cruz
authors.forename: Gaetano
authors.initials: G
authors.lastname: Tripoli
authors.forename: Marco
authors.initials: M
authors.lastname: Sardiello
authors.forename: Ivana
authors.initials: I
authors.lastname: Peluso
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
mesh_terms: D000818:Animals; D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics; D053595:Embryonic Stem Cells / Q000502:physiology*; D005091:Exons; D020224:Expressed Sequence Tags; D023281:Genomics; D007438:Introns; D051379:Mice / Q000235:genetics*; D008957:Models, Genetic; D010641:Phenotype; D012313:RNA / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: D012313:RNA