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This article is part of a special issue on epigenomics.

Open Access Method

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Patrick Boyle1, Kendell Clement1234, Hongcang Gu1, Zachary D Smith123, Michael Ziller123, Jennifer L Fostel1, Laurie Holmes1, Jim Meldrim1, Fontina Kelley1, Andreas Gnirke1 and Alexander Meissner123*

Author Affiliations

1 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

2 Harvard Stem Cell Institute, Cambridge, MA 02138, USA

3 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

4 Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA

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Genome Biology 2012, 13:R92  doi:10.1186/gb-2012-13-10-r92

Published: 3 October 2012

Abstract

Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage to the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies, including cohorts of cancer samples.