↓ Skip to main content

DNA Methylation Protocols

Overview of attention for book
Cover of 'DNA Methylation Protocols'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation
  3. Altmetric Badge
    Chapter 2 Considerations for Design and Analysis of DNA Methylation Studies
  4. Altmetric Badge
    Chapter 3 Quantification of Global DNA Methylation Levels by Mass Spectrometry
  5. Altmetric Badge
    Chapter 4 Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos
  6. Altmetric Badge
    Chapter 5 Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol
  7. Altmetric Badge
    Chapter 6 Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing
  8. Altmetric Badge
    Chapter 7 Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing
  9. Altmetric Badge
    Chapter 8 Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection
  10. Altmetric Badge
    Chapter 9 Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach
  11. Altmetric Badge
    Chapter 10 Methyl-CpG-Binding Domain Sequencing: MBD-seq
  12. Altmetric Badge
    Chapter 11 The HELP-Based DNA Methylation Assays
  13. Altmetric Badge
    Chapter 12 Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq
  14. Altmetric Badge
    Chapter 13 Digital Restriction Enzyme Analysis of Methylation (DREAM)
  15. Altmetric Badge
    Chapter 14 Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
  16. Altmetric Badge
    Chapter 15 Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)
  17. Altmetric Badge
    Chapter 16 A Guide to Illumina BeadChip Data Analysis
  18. Altmetric Badge
    Chapter 17 Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing
  19. Altmetric Badge
    Chapter 18 Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)
  20. Altmetric Badge
    Chapter 19 Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes
  21. Altmetric Badge
    Chapter 20 Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System
  22. Altmetric Badge
    Chapter 21 Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”
  23. Altmetric Badge
    Chapter 22 Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®
  24. Altmetric Badge
    Chapter 23 Methylation-Specific PCR
  25. Altmetric Badge
    Chapter 24 Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP) Assay
  26. Altmetric Badge
    Chapter 25 MethyLight and Digital MethyLight
  27. Altmetric Badge
    Chapter 26 Quantitative Region-Specific DNA Methylation Analysis by the EpiTYPER™ Technology
  28. Altmetric Badge
    Chapter 27 Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA)
  29. Altmetric Badge
    Chapter 28 Methylation-Sensitive High Resolution Melting (MS-HRM)
  30. Altmetric Badge
    Chapter 29 Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes
  31. Altmetric Badge
    Chapter 30 Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences
  32. Altmetric Badge
    Chapter 31 DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation Analysis
  33. Altmetric Badge
    Chapter 32 DNA Methylation Analysis of Free-Circulating DNA in Body Fluids
  34. Altmetric Badge
    Chapter 33 Tet-Assisted Bisulfite Sequencing (TAB-seq)
  35. Altmetric Badge
    Chapter 34 Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)
  36. Altmetric Badge
    Chapter 35 Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine
Attention for Chapter 21: Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”
Altmetric Badge

About this Attention Score

  • Average Attention Score compared to outputs of the same age
  • Good Attention Score compared to outputs of the same age and source (68th percentile)

Mentioned by

twitter
2 tweeters
facebook
1 Facebook page

Readers on

mendeley
21 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Chapter title
Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”
Chapter number 21
Book title
DNA Methylation Protocols
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7481-8_21
Pubmed ID
Book ISBNs
978-1-4939-7479-5, 978-1-4939-7481-8
Authors

Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, Andreas Weinhaeusel

Abstract

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.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 21 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 38%
Student > Bachelor 3 14%
Student > Master 3 14%
Researcher 2 10%
Lecturer > Senior Lecturer 1 5%
Other 0 0%
Unknown 4 19%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 10 48%
Medicine and Dentistry 3 14%
Agricultural and Biological Sciences 2 10%
Neuroscience 1 5%
Unknown 5 24%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 12 December 2017.
All research outputs
#8,038,712
of 13,345,024 outputs
Outputs from Methods in molecular biology
#2,556
of 8,476 outputs
Outputs of similar age
#201,689
of 386,613 outputs
Outputs of similar age from Methods in molecular biology
#458
of 1,662 outputs
Altmetric has tracked 13,345,024 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 8,476 research outputs from this source. They receive a mean Attention Score of 2.1. This one has gotten more attention than average, scoring higher than 66% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 386,613 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 44th percentile – i.e., 44% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,662 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 68% of its contemporaries.