Post-conversion targeted capture of modified cytosines in mammalian and plant genomes
Qing LiDepartment of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USAMasako SuzukiCenter for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USAJennifer WendtRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USANicole E. PattersonCenter for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USASteven R. EichtenDepartment of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USAPeter J. HermansonDepartment of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USADawn GreenRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USAJeffrey A. JeddelohRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USATodd RichmondRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USAHeidi RosenbaumRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USADaniel L. BurgessRoche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA [email protected]Nathan M. SpringerDepartment of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA [email protected]John M. GreallyCenter for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA [email protected]
2015en
ABI
Аннотация
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.
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