A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

Genomics
Geoffrey J FaulknerS M Grimmond

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.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Dec 6, 2002·Nature·Y OkazakiUNKNOWN RIKEN Genome Exploration Research Group Phase I & II Team
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Jun 24, 2003·Genome Research·Piero CarninciYoshihide Hayashizaki
Dec 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Toshiyuki ShirakiYoshihide Hayashizaki
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Sep 6, 2005·Science·P CarninciUNKNOWN RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
Apr 29, 2006·Nature Genetics·Piero CarninciYoshihide Hayashizaki
May 10, 2006·PLoS Genetics·Pär G EngströmLeonard Lipovich
May 10, 2006·PLoS Genetics·Vladimir B BajicYoshihide Hayashizaki
May 10, 2006·PLoS Genetics·Yoshihide Hayashizaki, Piero Carninci
May 12, 2006·Genome Research·Martin C FrithAlbin Sandelin
Jul 18, 2006·Nucleic Acids Research·Timothy L BaileyWilfred W Li
May 9, 2007·Nature Reviews. Genetics·Albin SandelinDavid A Hume

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Citations

Jul 12, 2014·BMC Genomics·Steven W CriscioneNicola Neretti
Dec 17, 2008·Genome Research·Eivind ValenPiero Carninci
Feb 25, 2009·Nucleic Acids Research·Katsuya TsuchiharaSumio Sugano
Aug 4, 2009·Bioinformatics·Nicole CloonanSean M Grimmond
Dec 22, 2009·Bioinformatics·Bo LiColin N Dewey
Sep 28, 2010·Bioinformatics·Jianrong WangI King Jordan
Feb 19, 2011·Bioinformatics·Marcus KinsellaVineet Bafna
Sep 9, 2011·Briefings in Bioinformatics·Jui-Hung HungCharles DeLisi
Apr 21, 2009·Nature Genetics·Ryan J TaftJohn S Mattick
Apr 21, 2009·Nature Genetics·Geoffrey J FaulknerPiero Carninci
Sep 23, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·David A Hume
Apr 12, 2011·FEBS Letters·Geoffrey J Faulkner
Jan 10, 2012·Science China. Life Sciences·Geng ChenTieliu Shi
Dec 1, 2009·Trends in Genetics : TIG·John S MattickGeoffrey J Faulkner
Jan 5, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Alka Saxena, Piero Carninci
Jul 14, 2010·Journal of Biomedicine & Biotechnology·Valerio CostaAlfredo Ciccodicola
Nov 24, 2012·Cancer Letters·Jiekun XuanLeming Shi
Jul 31, 2012·Methods : a Companion to Methods in Enzymology·Alison S DevonshireJim F Huggett
Feb 23, 2013·Neurobiology of Aging·Luba M PardoPeter Heutink
Jan 26, 2012·PloS One·Thomas DerrienPaolo Ribeca
Mar 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Kate SchroderMatthew J Sweet
Dec 27, 2016·Nature Biotechnology·Joris van ArensbergenBas van Steensel
Oct 26, 2018·Genome Research·Michael A SchonMichael D Nodine
Jan 10, 2019·Nucleic Acids Research·Wan R YangKathleen H Burns
Jun 3, 2008·Nature Methods·Nicole CloonanSean M Grimmond
May 14, 2016·G3 : Genes - Genomes - Genetics·Nathan R JohnsonMichael J Axtell
May 30, 2019·Bioinformatics·Gabrielle Deschamps-FrancoeurMichelle S Scott
Dec 28, 2019·Nucleic Acids Research·José Roberto Bermúdez-BarrientosCei Abreu-Goodger
Feb 12, 2017·BMC Bioinformatics·Arianna ConsiglioSabino Liuni
Mar 6, 2016·Science China. Life Sciences·Yuhui ZhaoSongnian Hu
Jul 14, 2018·Mobile DNA·Geoffrey J Faulkner, Victor Billon
May 6, 2020·International Journal of Molecular Sciences·Federica MarascaBeatrice Bodega

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