summary
Serial analysis of gene expression (SAGE) studies often yield numerous tags that cannot be mapped to known gene sequences. Intriguingly, these may represent unknown genes, unknown parts of genes, or transcript variants. In order to elucidate the origin of these tags, 3\(^\prime\)- and 5\(^\prime\)-rapid amplification of complementary DNA ends (RACE) reactions can be performed using primers identical or complementary to SAGE tags. This way, transcript fragments, or indeed the entire uncharacterized transcript, can be cloned and sequenced.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Reference
Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270, 484–487.
Saha, S., Sparks, A. B., Rago, C., et al. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–512.
Nielsen, K. L., Grønkjær, K., Welinder,K. G., and Emmersen,J. (2005) Global transcript profiling of potato tuber using LongSAGE. Plant Biotechnol. J. 3, 175–185.
Boheler, K. R. and Stern, M. D. (2003) The new role of SAGE in gene discovery. Trends Biotechnol. 21, 55–57.
Chen, J. J., Rowley, J. D., and Wang, S. M. (2000) Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proc. Natl. Acad. Sci. USA 97, 349–353.
Chen, J., Lee, S., Zhou, G., and Wang, S. M. (2002) High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3\(^\prime\) complementary DNAs. Genes Chromosomes Cancer 33, 252–261.
Frohman, M. A., Dush, M. K., and Martin, G. R. (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85, 8998–9002.
van den Berg, A., van der Leij, J. and Poppema, S. (1999) Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags. Nucleic Acids Res. 27, e17.
Elhafi, G., Naylor, C. J., Savage, C. E., and Jones, R. C. (2004) Microwave or autoclave treatments destroy the infectivity of infectious bronchitis virus and avian pneumovirus but allow detection by reverse transcriptase-polymerase chain reaction. Avian Pathol. 33, 303–306.
Crookshanks, M., Emmersen, J., Welinder, K. G., and Nielsen, K. L. (2001) The potato tuber transcriptome: analysis of 6077 expressed sequence tags. FEBS Lett. 506, 123–126.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Nielsen, K.L. (2008). \(^\prime\)- and 3\(^\prime\)-RACE from LongSAGE Tags. In: Nielsen, K.L. (eds) Serial Analysis of Gene Expression (SAGE). Methods in Molecular Biology™, vol 387. Humana Press. https://doi.org/10.1007/978-1-59745-454-4_8
Download citation
DOI: https://doi.org/10.1007/978-1-59745-454-4_8
Publisher Name: Humana Press
Print ISBN: 978-1-58829-676-4
Online ISBN: 978-1-59745-454-4
eBook Packages: Springer Protocols