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

29 Citations (Scopus)

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 - 2015

Fingerprint

Plant Genome
Cytosine
5-Methylcytosine
DNA
Genome
5-hydroxymethylcytosine
hydrogen sulfite

ASJC Scopus subject areas

  • Genetics

Cite this

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. / Li, Qing; Suzuki, Masako; Wendt, Jennifer; Patterson, Nicole; Eichten, Steven R.; Hermanson, Peter J.; Green, Dawn; Jeddeloh, Jeffrey; Richmond, Todd; Rosenbaum, Heidi; Burgess, Daniel; Springer, Nathan M.; Greally, John M.

In: Nucleic Acids Research, Vol. 43, No. 12, e81, 2015.

Research output: Contribution to journalArticle

Li, Q, Suzuki, M, Wendt, J, Patterson, N, Eichten, SR, Hermanson, PJ, Green, D, Jeddeloh, J, Richmond, T, Rosenbaum, H, Burgess, D, Springer, NM & Greally, JM 2015, 'Post-conversion targeted capture of modified cytosines in mammalian and plant genomes', Nucleic Acids Research, vol. 43, no. 12, e81. https://doi.org/10.1093/nar/gkv244
Li, Qing ; Suzuki, Masako ; Wendt, Jennifer ; Patterson, Nicole ; Eichten, Steven R. ; Hermanson, Peter J. ; Green, Dawn ; Jeddeloh, Jeffrey ; Richmond, Todd ; Rosenbaum, Heidi ; Burgess, Daniel ; Springer, Nathan M. ; Greally, John M. / Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 12.
@article{b81148df4a7540f1b76be16bb566bed8,
title = "Post-conversion targeted capture of modified cytosines in mammalian and plant genomes",
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.",
author = "Qing Li and Masako Suzuki and Jennifer Wendt and Nicole Patterson and Eichten, {Steven R.} and Hermanson, {Peter J.} and Dawn Green and Jeffrey Jeddeloh and Todd Richmond and Heidi Rosenbaum and Daniel Burgess and Springer, {Nathan M.} and Greally, {John M.}",
year = "2015",
doi = "10.1093/nar/gkv244",
language = "English (US)",
volume = "43",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "12",

}

TY - JOUR

T1 - Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

AU - Li, Qing

AU - Suzuki, Masako

AU - Wendt, Jennifer

AU - Patterson, Nicole

AU - Eichten, Steven R.

AU - Hermanson, Peter J.

AU - Green, Dawn

AU - Jeddeloh, Jeffrey

AU - Richmond, Todd

AU - Rosenbaum, Heidi

AU - Burgess, Daniel

AU - Springer, Nathan M.

AU - Greally, John M.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84942244533&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84942244533&partnerID=8YFLogxK

U2 - 10.1093/nar/gkv244

DO - 10.1093/nar/gkv244

M3 - Article

VL - 43

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 12

M1 - e81

ER -