Skip to main content

Part of the book series: Methods in Molecular Biology ((MIMB,volume 37))

Abstract

Subtraction-hybridization cDNA libraries (14) are libraries enriched for sequences representing mRNAs whose expression in one biological source (e.g., tissues, cell lines) is different than in a second source. Single-stranded cDNAs from both sources are allowed to hybridize so that sequences common to the two sources will anneal. The annealed, double-stranded DNAs are “subtracted” from the hybridization solution, leaving a population of cDNA molecules enriched for sequences preferentially expressed (or repressed) in the biological source of interest. Figure 1 diagrammatically represents the scheme for subtraction hybridization currently employed in our laboratory.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Schweinfest, W., Henderson, K. W., Gu, J.-R., Kottaridis, S. D., Besbeas, S., Panatopoulou, E., and Papas, T. S. (1990) Subtraction hybridization cDNA libraries from colon carcinoma and hepatic cancer. Genet. Anal. Techn. Appl. 7, 64–70.

    Article  CAS  Google Scholar 

  2. Duguid, J., Rohwer, R. G., and Seed, B. (1988) Isolation of cDNAs of scraptemodulated RNAs by subtractive hybridization of a cDNA library. Proc. Natf. Acad. Sci. USA 85, 5738–5742.

    Article  CAS  Google Scholar 

  3. Rubenstein, J. L. R., Brice, A. E. J., Ciaranello, R. D., Denney, D., Porteus, M. H., and Usdin, T. B.,(1990) Subtractive hybridization system using single-stranded phagemids with directional inserts. Nucleic Acids Res. 18, 4833–4842.

    Article  PubMed  CAS  Google Scholar 

  4. Owens, G. P., Hahn, W. E., and Cohen, J. J. (1991) Identification of mRNAs associated with programmed cell death in immature thymocytes. Mol. Cell. Biol. 11, 4177–4188.

    PubMed  CAS  Google Scholar 

  5. Lau, L. F. and Nathans, D. (1985) Identification of a set of genes expressed during the G0/G1 transition of cultured mouse cells. EMBO J. 4, 3145–3151.

    PubMed  CAS  Google Scholar 

  6. Hirschhorn, R. R., Aller, P., Yuan, Z.-A., Gibson, W., and Baserga, R. (1984) Cell-cycle-specific cDNAs from mammalian cells temperature sensitive for growth. Proc. Natl. Acad. Sci. USA 81, 6004–6008.

    Article  PubMed  CAS  Google Scholar 

  7. Chirgwin, J. M., Przybyla, A. E., MacDonald, R. J., and Rutter, W. J. (1979) Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18, 5294–5299.

    Article  PubMed  CAS  Google Scholar 

  8. Gubler, U. and Hoffman, B. J. (1983) A simple and very efficient method for generating cDNA libraries. Gene 25, 263–269.

    Article  PubMed  CAS  Google Scholar 

  9. Sambrook, J., Fritsch, E. F., and Maniatis, T., eds. (1989) Molecular Cloning: A Laboratory Markal, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

    Google Scholar 

  10. Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159.

    Article  PubMed  CAS  Google Scholar 

  11. Nelson, P. S., Papas, T. S., and Schweinfest, C. W. (1993) Restriction endonuclease cleavage of 5-methyl-deoxycy tosine hemimethylated DNA at high enzyme-to-substrate ratios. Nucleic Acids Res. 21, 681–686.

    Article  PubMed  CAS  Google Scholar 

  12. Brennan, A., Van Cleve, M. D., and Gumport, R. I. (1986) The effects of base analogue substitutions on the cleavage by RI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261, 7270–7278.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Humana Press Inc.

About this protocol

Cite this protocol

Schweinfest, C.W., Nelson, P.S., Graber, M.W., Demopoulos, R.I., Papas, T.S. (1995). Subtraction Hybridization cDNA Libraries. In: Tymms, M.J. (eds) In Vitro Transcription and Translation Protocols. Methods in Molecular Biology, vol 37. Humana Press. https://doi.org/10.1385/0-89603-288-4:13

Download citation

  • DOI: https://doi.org/10.1385/0-89603-288-4:13

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-288-0

  • Online ISBN: 978-1-59259-524-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics