Genome wide mapping of methylated and hydroxyl-methylated cytosines using a modified hpaii tiny fragment enrichment by ligation mediated PCR tagged sequencing protocol

Sanchari Battachariyya, Ruslana Tytarenko, Christoph Heuck, John M. Greally, Amit K. Verma

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Abstract

Here we describe a method for genome wide investigation of methylation and hydroxymethylation status of cytosines. This protocol is an improvement of the HELP-tagging protocol previously described by Suzuki et al. It involves the glucosylation of 5-hydroxymethylcytosines (5-hmC) with β-glucosyl transferase (β-GT), thus rendering them resistant to digestion by MspI. Parallel digestion of β-GT treated samples with MspI, untreated sample with MspI and another untreated sample with HpaII, followed by adapter ligation, parallel sequencing and bioinformatics processing results in a differential display of MspI digestion sites that allows the determination of the distribution of 5-methylcytosines (5-mC) and 5-hmC at these sites.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages167-177
Number of pages11
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1792
ISSN (Print)1064-3745

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Keywords

  • 5-hydroxymethylcytosine
  • 5-methylcytosine
  • DNA methylation
  • HpaII
  • MspI
  • Sequencing
  • β-glucosyl transferase

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Battachariyya, S., Tytarenko, R., Heuck, C., Greally, J. M., & Verma, A. K. (2018). Genome wide mapping of methylated and hydroxyl-methylated cytosines using a modified hpaii tiny fragment enrichment by ligation mediated PCR tagged sequencing protocol. In Methods in Molecular Biology (pp. 167-177). (Methods in Molecular Biology; Vol. 1792). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7865-6_12