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 Citation (Scopus)

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

Fingerprint

Chromosome Mapping
Cytosine
Hydroxyl Radical
Ligation
Digestion
Polymerase Chain Reaction
5-Methylcytosine
Transferases
Computational Biology
Methylation
Genome
5-hydroxymethylcytosine

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

Genome wide mapping of methylated and hydroxyl-methylated cytosines using a modified hpaii tiny fragment enrichment by ligation mediated PCR tagged sequencing protocol. / Battachariyya, Sanchari; Tytarenko, Ruslana; Heuck, Christoph; Greally, John M.; Verma, Amit K.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 167-177 (Methods in Molecular Biology; Vol. 1792).

Research output: Chapter in Book/Report/Conference proceedingChapter

Battachariyya, Sanchari ; Tytarenko, Ruslana ; Heuck, Christoph ; Greally, John M. ; Verma, Amit K. / Genome wide mapping of methylated and hydroxyl-methylated cytosines using a modified hpaii tiny fragment enrichment by ligation mediated PCR tagged sequencing protocol. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 167-177 (Methods in Molecular Biology).
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