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.”
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References
Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc NutE. Acad. Sci. USA 81, 1991–1995
Maxam, A. M and Gilbert, W (1980) Sequencing end-labeled DNA with basespecific chemical cleavages. Methods Enzymol. 65, 499–560.
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
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.
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
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.
Mueller, P R. and Wold, B. (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246, 780–786.
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.
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.
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.
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
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
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.
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.
Saluz, H. P. and Jost, J. P. (1987) A Laboratory guide to genomic sequencing Birkhauser, Boston
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.
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
Stiirzl, M. and Roth, W. K. (1990) “Run-off” synthesis and application of defined single-stranded DNA hybridization probes. Anal. Blochem. 185, 164–169.
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.
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© 1993 Humana Press Inc. Totowa, New Jersey
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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
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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
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