The HELP-based DNA methylation assays

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations


Restriction enzymes have been valuable tools for representing the genome for DNA methylation assays, whether by using methylation-dependent enzymes or by sampling a reduced representation of the genome using a methylation-insensitive enzyme. These survey assays have remained mainstays of genome-wide approaches even with the development of more comprehensive shotgun genome-wide bisulphite sequencing-based assays, as they are significantly more affordable. DNA methylation survey assays are numerous and include reduced representation bisulphite sequencing (RRBS), the Illumina HumanMethylation450K and EPIC microarray system, and our evolving series of HELP-based assays. The HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR) assays initially involved microarray-based reporting of DNA methylation, but have now migrated to the use of massively parallel sequencing. In this chapter, we describe the latest HELP-tagging assay that uses Illumina Tru-Seq adapters, and mention the extension of the HELP-tagging assay to quantify 5-hydroxymethylation using the HELP-GT assay.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages17
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • CpG dinucleotide
  • Cytosine methylation
  • Epigenetic
  • Epigenome
  • Massively parallel sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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