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 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.
authors: Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA.
authors: Qing
authors: Q
authors: Li
authors: Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
authors: Masako
authors: M
authors: Suzuki
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA.
authors: Jennifer
authors: J
authors: Wendt
authors: Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.
authors: Nicole
authors: N
authors: Patterson
authors: Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA.
authors: Steven R
authors: SR
authors: Eichten
authors: Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA.
authors: Peter J
authors: PJ
authors: Hermanson
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA.
authors: Dawn
authors: D
authors: Green
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA.
authors: Jeffrey
authors: J
authors: Jeddeloh
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA.
authors: Todd
authors: T
authors: Richmond
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA.
authors: Heidi
authors: H
authors: Rosenbaum
authors: Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA daniel.burgess@roche.com.
authors: Daniel
authors: D
authors: Burgess
authors: Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA springer@umn.edu.
authors: Nathan M
authors: NM
authors: Springer
authors: Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA john.greally@einstein.yu.edu.
authors: John M
authors: JM
authors: Greally
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis* / Q000031:analogs & derivatives; D000483:Alleles; D000818:Animals; D002460:Cell Line; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D019175:DNA Methylation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites
chemical_list: D013447:Sulfites; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; C042345:hydrogen sulfite