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

Research output: Contribution to journalArticle

33 Scopus citations

Abstract

We present a capture-based approach for bisulfite-converted DNA that allows interrogation of predefined 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.

Original languageEnglish (US)
Article numbere81
JournalNucleic acids research
Volume43
Issue number12
DOIs
StatePublished - Jan 1 2015

    Fingerprint

ASJC Scopus subject areas

  • Genetics

Cite this

Li, Q., Suzuki, M., Wendt, J., Patterson, N., Eichten, S. R., Hermanson, P. J., Green, D., Jeddeloh, J., Richmond, T., Rosenbaum, H., Burgess, D., Springer, N. M., & Greally, J. M. (2015). Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic acids research, 43(12), [e81]. https://doi.org/10.1093/nar/gkv244