Skip to main content

Genomic Sequencing

  • Protocol
DNA Sequencing Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 23))

Abstract

The cloning of eukaryotic DNA in bacteria or by the polymerase chain reaction (PCR) inevitably results in the loss of much information, Protein-DNA contacts and cytosine methylation patterns, both important in gene regulation and other cellular processes, are not reproduced in these cloning procedures. To retain information on cytosine methylation and protein footprints, the DNA has to be sequenced in its native genomic state. Direct sequencing of genomic DNA followed by detection of specific sequences is referred to here to as “Genomic Sequencing.”

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. Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc NutE. Acad. Sci. USA 81, 1991–1995

    Article  CAS  Google Scholar 

  2. Maxam, A. M and Gilbert, W (1980) Sequencing end-labeled DNA with basespecific chemical cleavages. Methods Enzymol. 65, 499–560.

    Article  PubMed  CAS  Google Scholar 

  3. Kochanek, S., Toth, M., Dehmel, A., Renz, D., and Doerfler, W. (1990) Interindividual concordance of methylation profiles m human genes for tumor necrosis factor alpha and beta Proc. Natl. Acad. Scr USA 87, 8830–8834

    Article  CAS  Google Scholar 

  4. Mirkovitch, J. and Darnell, J. E., Jr. (1991) Rapid m VIVO footprinting technique identifies protems bound to the TTR gene m the mouse liver. Genes Dev. 5, 83–93.

    Article  PubMed  CAS  Google Scholar 

  5. Axelrod, J. D and Majors, J. (1989) An improved method for photofootprintmg yeast genes in vivo using Tag polymerase Nucl. Acids Res. 17, 171–183

    Article  PubMed  CAS  Google Scholar 

  6. Saluz, H. and Jost, J. P. (1989) A simple htgh-resolution procedure to study DNA methylatton and in vivo DNA-protein mteractions on a single-copy gene level in higher eukaryotes. Proc Natl. Acad Sci. USA 86, 2602–2606.

    Article  PubMed  CAS  Google Scholar 

  7. Mueller, P R. and Wold, B. (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246, 780–786.

    Article  PubMed  CAS  Google Scholar 

  8. Pfeifer, G. P, Steigerwald, S. D., Mueller, P. R., Weld, B., and Riggs, A. D (1989) Genomic sequencing and methylation analysts by ligation medtated PCR. Science 246, 810–813.

    Article  PubMed  CAS  Google Scholar 

  9. Pfeifer, G. P., Tanguay, R. L., Steigerwald, S. D, and Rtggs, A D (1990) In vivo footprint and methylation analysis by PCR-aided genomic sequencing. comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. Genes Dev. 4, 1277–1287.

    Article  PubMed  CAS  Google Scholar 

  10. Pfeifer, G P., Steigerwald, S. D, Hansen, R S., Gartler, S. M., and Riggs, A D. (1990) Polymerase chain reaction aided genomtc sequencing of an X chromosome-linked CpG island. Methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanatton of activity state stability Proc Natl Acad. Sci. USA 87, 8252–8256.

    Article  PubMed  CAS  Google Scholar 

  11. Rideout, W. M., III, Coetzee, G. A., Olumi, A. F, and Jones, P A. (1990) 5 Methylcytosine as an endogenous mutagen in the human LDL receptor and ~53 genes. Science 249, 1288–1290

    Article  PubMed  CAS  Google Scholar 

  12. Pfeifer, G. P., Droum, R., Riggs, A. D., and Holmqmst, G. P. (1991) In vivo mapping of a DNA adduct at nucleotide resolution. detection of pyrimidine (64) pyrimidone photoproducts by hgation-mediated polymerase chain reaction Proc. Nat1 Acad. Sci USA88, 1374–1378

    Article  CAS  Google Scholar 

  13. Pfeifer, G. P. and Riggs, A. D. (1991) Chromatin differences between active and inactive X chromosomes revealed by genomic footprintmg of permeabilized cells using DNase I and hgation-mediated PCR. Genes Dev. 5, 1102–1113.

    Article  PubMed  CAS  Google Scholar 

  14. Rychlik, W., and Rhoads, R E (1989) A computer program for choosing optimal ohgonucleotides for filter hybrtdlzation, sequencing and in vitro amplification of DNA. Nucl Acids Res. 17, 8543–8551.

    Article  PubMed  CAS  Google Scholar 

  15. Saluz, H. P. and Jost, J. P. (1987) A Laboratory guide to genomic sequencing Birkhauser, Boston

    Google Scholar 

  16. Gross, D S., Collins, K. W, Hernandez, E. M, and Garrard, W. T. (1988) Vacuum blotting: a simple method for transfering DNA from sequencing gels to nylon membranes. Gene 74, 347–356.

    Article  PubMed  CAS  Google Scholar 

  17. Weih, F., Stewart, A F., and Schtitz, G. (1988) A novel and rapid method to generate single stranded DNA probes for genomic footprmtmg. Nucl Acids Res. 16, 1628

    Article  PubMed  CAS  Google Scholar 

  18. Stiirzl, M. and Roth, W. K. (1990) “Run-off” synthesis and application of defined single-stranded DNA hybridization probes. Anal. Blochem. 185, 164–169.

    Article  Google Scholar 

  19. Tormanen, V T. and Pfeifer, G. P. (1992) Mapping of UV photoproducts within ras proto-oncogenes in UV-irradiated cells: correlation with mutations in human skin cancer. Oncogene 7, 1729–1736.

    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

© 1993 Humana Press Inc. Totowa, New Jersey

About this protocol

Cite this protocol

Pfeifer, G.P., Riggs, A.D. (1993). Genomic Sequencing. In: Griffin, H.G., Griffin, A.M. (eds) DNA Sequencing Protocols. Methods in Molecular Biology™, vol 23. Humana Press. https://doi.org/10.1385/0-89603-248-5:169

Download citation

  • DOI: https://doi.org/10.1385/0-89603-248-5:169

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-248-4

  • Online ISBN: 978-1-59259-510-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics