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Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”

Part of the Methods in Molecular Biology book series (MIMB,volume 1708)


DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully. Even though epigenome-wide discovery of altered DNA methylation patterns has found its way into various fields of human disease and molecular genetics research, the validation of findings upon discovery is still a bottleneck. Usually several multiples of 10 up to 100 candidate biomarkers from discovery have to be confirmed or are of interest for further work. In particular, bisulfite PCR assays are often limited in the number of candidates which can be analyzed, due to their low multiplexing capability, especially, if only small amounts of DNA are available from for example clinical specimens. In clinical research and diagnostics a similar situation arises for the analyses of cell-free DNA (cfDNA) in body fluids or circulating tumor cells (CTCs). Although tissue- or disease- (e.g., cancer) specific DNA methylation patterns can be deduced very efficiently in a genome-wide manner if around 100 ng of DNA are available, confirming these candidates and selecting target-sequences for studying methylation changes in liquid biopsies using cfDNA or CTCs remains a big challenge. Along these lines we have developed MSRE-qPCR and introduce here method details, which have been found very suitable for the efficient confirmation and testing of DNA methylation in a quantitative multiplexed manner (e.g., 48–96 plex) from ng amounts of DNA. The method is applicable in a standard qPCR setting as well for nanoliter scaled high-throughput qPCR, enabling detection of <10 copies of targets, thus suitable to pick up 0.1–1% of specific methylated DNA in an unmethylated background.

Key words

  • Methylation-sensitive restriction enzyme
  • Multiplex
  • qPCR
  • DNA methylation

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We thank former colleagues Rudolf Pichler, Markus Sonntagbauer, Elisabeth Reithuber, and Matthias Wielscher involved in developing and improving the described MSRE-qPCR approach. Part of this work was supported by: European Community’s Seventh Framework program EurHEALTHAgeing HEALTH-F2-2011-277849 and RESOLVE FP7-HEALTH-F4-2008-202047.

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Correspondence to Andreas Weinhaeusel .

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Beikircher, G., Pulverer, W., Hofner, M., Noehammer, C., Weinhaeusel, A. (2018). Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”. In: Tost, J. (eds) DNA Methylation Protocols. Methods in Molecular Biology, vol 1708. Humana Press, New York, NY.

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  • Print ISBN: 978-1-4939-7479-5

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