Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing

Nature Biotechnology
Blake C MeyersChristian D Haudenschild

Abstract

Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.

References

Oct 20, 1995·Science·V E VelculescuK W Kinzler
Jul 1, 1997·Nucleic Acids Research·G Edwalds-GilbertC Milcarek
Oct 23, 1997·Genome Research·S Audic, J M Claverie
May 29, 1998·Gene·C Vanhée-Brossollet, C Vaquero
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·S BrennerG Albrecht
Jun 29, 2000·Biochemical and Biophysical Research Communications·L Knirsch, L B Clerch
Sep 6, 2000·Trends in Plant Science·N Terryn, P Rouzé
Oct 24, 2000·Genome Research·R GuigóJ W Fickett
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
Jan 31, 2002·Trends in Genetics : TIG·Ben LehnerChristopher M Sanderson
May 4, 2002·Science·Philipp KapranovThomas R Gingeras
Jun 5, 2002·Annual Review of Biochemistry·Brenda L Bass
Jul 5, 2002·Genome Research·Christian IseliC Victor Jongeneel
Aug 29, 2002·The EMBO Journal·Yoontae LeeV Narry Kim
Oct 9, 2002·The Plant Journal : for Cell and Molecular Biology·Blake C MeyersRichard W Michelmore
Dec 14, 2002·Plant Physiology·Yong-Li XiaoChristopher D Town
Jun 14, 2003·The EMBO Journal·Victor QuesadaGordon G Simpson
Jun 14, 2003·Plant Physiology·Jennifer R WortmanChristopher D Town
Sep 23, 2003·Nucleic Acids Research·Brian J HaasOwen White
Nov 1, 2003·Science·Kayoko YamadaJoseph R Ecker
Nov 20, 2003·Nature Genetics·Victoria Perepelitsa-Belancio, Prescott Deininger
Dec 13, 2003·Science·Kenneth BirnbaumPhilip N Benfey
Aug 4, 2004·Genome Research·Blake C MeyersShannon Decola
Dec 14, 2006·Plant Biotechnology Journal·J George GibbingsJim M Dunwell

❮ Previous
Next ❯

Citations

Oct 8, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Paulo P Amaral, John S Mattick
Jun 21, 2007·Molecular Genetics and Genomics : MGG·R C VenuGuo-Liang Wang
Oct 31, 2012·Molecular Genetics and Genomics : MGG·Xiaohui WuYong Zeng
Apr 11, 2007·Nature Biotechnology·Antoni Rafalski
Aug 3, 2004·Nature Biotechnology·Jeffrey F D Dean
Mar 14, 2007·Nature Biotechnology·Kan NobutaBlake C Meyers
Jul 24, 2012·Nature Structural & Molecular Biology·Alexander SherstnevGordon G Simpson
Jul 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui WuArthur G Hunt
Mar 24, 2012·Journal of Experimental Botany·Nidia Sánchez-LeónJean-Philippe Vielle-Calzada
Jul 15, 2006·Nucleic Acids Research·Asim S SiddiquiMarco A Marra
Dec 20, 2007·Nucleic Acids Research·UNKNOWN Rice Annotation ProjectManuel Echeverria
Apr 16, 2008·Nucleic Acids Research·Yingjia ShenQingshun Quinn Li
Aug 4, 2004·Genome Research·Blake C MeyersShannon Decola
Mar 8, 2006·Genome Research·Christopher MaherDoreen Ware
Jun 3, 2004·Plant Physiology·Blake C MeyersLarry D Tindell
Jun 3, 2004·Plant Physiology·Blake C MeyersVikas Agrawal
Aug 10, 2006·Plant Physiology·Aleel K Grennan
Nov 14, 2006·Plant Physiology·Siobhan M BradyPhilip N Benfey
Feb 27, 2007·Plant Physiology·Gabriel LeónXavier Jordana
May 15, 2007·Plant Physiology·Stefan R HenzMarkus Schmid
Oct 24, 2007·Plant Physiology·Margit MengesJames A H Murray
Jan 7, 2005·The Plant Journal : for Cell and Molecular Biology·H Stanley KimJohn Quackenbush
Jan 22, 2008·Biochemistry. Biokhimii︠a︡·I V GainetdinovE D Sverdlov
May 4, 2006·Annual Review of Plant Biology·David W Galbraith, Kenneth Birnbaum
Feb 9, 2007·BMC Bioinformatics·Guoli JiQingshun Quinn Li
Dec 22, 2010·BMC Genomics·Yijun MengMing Chen

❮ Previous
Next ❯

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