title: Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments.
abstract: Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemical treatment causes strand scission, which depletes the number of sequenceable DNA fragments in a library and thus necessitates PCR amplification. The AT-rich nature of the library generated from bisulfite treatment adversely affects this amplification, resulting in the introduction of major biases that can confound methylation analysis. Here, we report a method that enables more accurate methylation analysis, by rebuilding bisulfite-damaged components of a DNA library. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We apply the ReBuilT method for the first whole methylome analysis of the highly AT-rich genome of Plasmodium berghei. Side-by-side comparison to a commercial protocol involving amplification demonstrates a substantial improvement in uniformity of coverage and reduction of sequence context bias. Our method will be widely applicable for quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Gordon R
authors.initials: GR
authors.lastname: McInroy
authors.affiliation: Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Dario
authors.initials: D
authors.lastname: Beraldi
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Eun-Ang
authors.initials: EA
authors.lastname: Raiber
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Modrzynska
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Pieter
authors.initials: P
authors.lastname: van Delft
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Oliver
authors.initials: O
authors.lastname: Billker
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.|Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, Cambridgeshire, United Kingdom.|School of Clinical Medicine, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Shankar
authors.initials: S
authors.lastname: Balasubramanian
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid; D018899:CpG Islands; D004247:DNA / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D019175:DNA Methylation; D015723:Gene Library; D010962:Plasmodium berghei / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000737:chemistry; D053719:Tandem Mass Spectrometry
chemical_list: D013447:Sulfites; D044503:5-Methylcytosine; D004247:DNA; C042345:hydrogen sulfite