SuperSAGE as an Analytical Tool for Host and Viral Gene Expression

  • Hideo MatsumuraEmail author
  • Detlev H. Krüger
  • Günter Kahl
  • Ryohei Terauchi
Part of the Methods in Molecular Biology book series (MIMB, volume 1236)


SuperSAGE is a tag-based transcript profiling method, which allows to analyze the expression of thousands of genes at a time. In SuperSAGE, 26 bp tags are extracted from cDNA using the type III restriction enzyme, EcoP15I. In SuperSAGE, the amount of transcripts was represented by tag counts. Taking advantage of uniqueness of the 26 bp tags, host and virus transcripts can be monitored in virus-infected cells. Combining next generation sequencing technology, we established High-throughput SuperSAGE (Ht-SuperSAGE), which allows the analysis of multiple samples with reduced time and cost. In this chapter, we present the protocol of Ht-SuperSAGE involving a recently available benchtop type next generation sequencer.

Key words

SuperSAGE Next generation sequencing Transcriptome Host-pathogen interaction Gene expression 



HM is supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN). This work is also supported by JSPS (Japan Society for the Promotion of Science) grant no. 25450004.


  1. 1.
    Schena M, Shalon D, Davis RW, Brown PQ (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470PubMedCrossRefGoogle Scholar
  2. 2.
    Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  3. 3.
    Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487PubMedCrossRefGoogle Scholar
  4. 4.
    Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger DH, Terauchi R (2003) Gene expression analysis of host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci U S A 100:15718–15723PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Matsumura H, Reuter M, Krüger DH, Winter P, Kahl G, Terauchi R (2007) SuperSAGE. Meth Mol Biol 387:55–70CrossRefGoogle Scholar
  6. 6.
    Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553PubMedCrossRefPubMedCentralGoogle Scholar
  7. 7.
    Matsumura H, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger D, Terauchi R (2005) SuperSAGE. Cell Microbiol 7:11–18PubMedCrossRefGoogle Scholar
  8. 8.
    Raftery MJ, Möncke-Buchner E, Matsumura H, Giese T, Winkelmann A, Reuter M, Terauchi R, Schönrich G, Krüger DH (2009) Unravelling the interaction of human cytomegalovirus with dendritic cells by using SuperSAGE. J Gen Virol 90:2221–2233PubMedCrossRefGoogle Scholar
  9. 9.
    Hamada H, Matsumura H, Tomita R, Terauchi R, Suzuki K, Kobayashi K (2008) SuperSAGE revealed different classes of early resistance response genes in Capsicum chinense plants harboring L 3-resistance gene infected with Pepper mild mottle virus. J Gen Plant Pathol 74:313–321CrossRefGoogle Scholar
  10. 10.
    Matsumura H, Nasir KHB, Yoshida K, Ito A, Kahl G, Krüger DH, Terauchi R (2006) SuperSAGE-array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Meth 3:469–474CrossRefGoogle Scholar
  11. 11.
    Nasir KH, Takahashi Y, Ito A, Saitoh H, Matsumura H, Kanzaki H, Shimizu T, Ito M, Fujisawa S, Sharma PC, Ohme-Takagi M, Kamoun S, Terauchi R (2005) High-throughput in planta expression screening identifies a class II ethylene-responsive element binding factor-like protein that regulates plant cell death and non-host resistance. Plant J 43:491–505PubMedCrossRefGoogle Scholar
  12. 12.
    Matsumura H, Yoshida K, Luo S, Kimura E, Fujibe T, Albertyn Z, Barrero RA, Krüger DH, Kahl G, Schroth GP, Terauchi R (2010) High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing. PLoS One 5:e1201Google Scholar
  13. 13.
    Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, Kahl G (2011) The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biol 11:31PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Bonaventure G (2010) SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses. BMC Plant Biol 10:66PubMedCrossRefPubMedCentralGoogle Scholar
  15. 15.
    Sharbel TF, Voigt ML, Corral JM, Galla G, Kumlehn J, Klukas C, Schreiber F, Vogel H, Rotter B (2010) Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell 22:655–671PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Gilardoni PA, Schuck S, Jüngling R, Rotter B, Baldwin IT, Zawada AM, Rogacev KS, Rotter B, Winter P, Marell RR, Fliser D, Heine GH (2011) SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset. Blood 118:e50–e61CrossRefGoogle Scholar
  17. 17.
    Kahl G, Molina C, Rotter B, Jüngling R, Frank A, Krezdorn N, Hoffmeier K, Winter P (2012) Reduced representation sequencing of plant stress transcriptomes. J Plant Biochem Biotech 21:119–127CrossRefGoogle Scholar
  18. 18.
    Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C (2013) Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. Front Plant Sci 4:423PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517PubMedCrossRefPubMedCentralGoogle Scholar
  20. 20.
    Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250–255PubMedCrossRefGoogle Scholar
  21. 21.
    Westermann AJ, Gorski SA, Vogel J (2012) Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10:618–630PubMedCrossRefGoogle Scholar
  22. 22.
    Matsumura H, Yoshida K, Luo S, Krüger DH, Kahl G, Schroth GP, Terauchi R (2011) High-throughput SuperSAGE. Meth Mol Biol 687:135–148CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Hideo Matsumura
    • 1
    Email author
  • Detlev H. Krüger
    • 2
  • Günter Kahl
    • 3
  • Ryohei Terauchi
    • 4
  1. 1.Gene Research CenterShinshu UniversityUedaJapan
  2. 2.Institute of Medical VirologyCharité Universitätsmedizin BerlinBerlinGermany
  3. 3.BiocenterUniversity of Frankfurt am MainFrankfurtGermany
  4. 4.Iwate Biotechnology Research CenterKitakamiJapan

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