Bisulfite Sequencing of Cloned Alleles

  • Zhiqing Huang
  • Christopher F. Bassil
  • Susan K. Murphy
Part of the Methods in Molecular Biology book series (MIMB, volume 1049)


Bisulfite sequencing of cloned alleles is a widely used method for capturing the methylation profiles of single alleles. This method combines PCR amplification of the bisulfite-modified DNA with the subcloning of the amplicons into plasmids followed by transformation into bacteria and plating on selective media. The resulting colony forming units are each comprised of bacterial clones containing the same plasmid reflecting a single allele in the original PCR reaction. Following whole cell PCR and sequencing, the results provide highly detailed information about the status of each CG site within an allele. Sequencing of a large number of individual clones can provide quantitative information, assuming unbiased PCR, subcloning and clone selection. The proportion of methylated cytosine at a particular position within the sequenced alleles can be determined by counting the number of alleles showing methylation at the position of interest and dividing this by the total number of clones sequenced.

Key words

DNA methylation Sodium bisulfite Cloning Capillary sequencing 



We gratefully acknowledge Zack Davenport for his contributions to the artwork. We thank Allison Barratt and Carole Grenier for critical reading of the manuscript. This work was supported by Department of Defense grant W81XWH-11-1-0469, NIH grants R01DK085173 and R01CA142983 and the Gail Parkins Ovarian Cancer Awareness Fund.


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Copyright information

© Springer Science+Business Media, New York 2013

Authors and Affiliations

  • Zhiqing Huang
    • 1
  • Christopher F. Bassil
    • 1
  • Susan K. Murphy
    • 1
  1. 1.Division of Gynecologic OncologyDuke University Medical CenterDurhamUSA

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