Nucleic Acids Research 2015-07-13

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.

Qing Li, Masako Suzuki, Jennifer Wendt, Nicole Patterson, Steven R Eichten, Peter J Hermanson, Dawn Green, Jeffrey Jeddeloh, Todd Richmond, Heidi Rosenbaum, Daniel Burgess, Nathan M Springer, John M Greally

Index: Nucleic Acids Res. 43 , e81, (2015)

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Abstract

We present a capture-based approach for bisulfite-converted DNA that allows interrogation of pre-defined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.