Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing

Aniruddha Chatterjee; Euan J Rodger; Peter A Stockwell; Gwenn Le Mée; Ian M Morison

doi:10.1007/978-1-4939-6685-1_16

Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing

Methods Mol Biol. 2017:1537:279-298. doi: 10.1007/978-1-4939-6685-1_16.

Authors

Aniruddha Chatterjee^{1

2}, Euan J Rodger³, Peter A Stockwell⁴, Gwenn Le Mée³, Ian M Morison^{5

6}

Affiliations

¹ Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. [email protected].
² Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand. [email protected].
³ Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
⁴ Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9054, New Zealand.
⁵ Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. [email protected].
⁶ Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand. [email protected].

PMID: 27924600
DOI: 10.1007/978-1-4939-6685-1_16

Abstract

Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes. Furthermore, we provide a brief guideline for base-calling and data analysis of multiplexed RRBS libraries. These strategies will be useful to perform large-scale, genome-wide DNA methylation analysis.

Keywords: CpG island; DMAP; DNA methylation; Epigenetics; Multiplexed; Reduced representation bisulfite sequencing; Second-generation sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
CpG Islands
DNA Methylation*
Epigenomics / methods*
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Humans
Polymerase Chain Reaction
Sequence Analysis, DNA*
Software
Transcriptome*
Web Browser