title: A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.
abstract: Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of protein-coding mouse transcriptional frameworks detected by CAGE improved from 42.9 to 57.8% (an increase of 5516 frameworks) with no reduction in CAGE to microarray correlation. These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone.
authors.affiliation: The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia. g.faulkner@imb.uq.edu.au
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Faulkner
authors.forename: Alistair R R
authors.initials: AR
authors.lastname: Forrest
authors.forename: Alistair M
authors.initials: AM
authors.lastname: Chalk
authors.forename: Kate
authors.initials: K
authors.lastname: Schroder
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012315:RNA Caps / Q000235:genetics; D016324:Sequence Tagged Sites; D024363:Transcription Initiation Site
chemical_list: D018076:DNA, Complementary; D012315:RNA Caps