title: Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells.
abstract: 5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals at base resolution. Implementing this approach, termed "TAB-array", we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular progenitors and neural precursor cells. With the ability to discriminate 5mC and 5hmC, we identified a large number of novel dynamically methylated genomic regions that are implicated in the development of these lineages. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: Kristopher L
authors.initials: KL
authors.lastname: Nazor
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Boland
authors.affiliation: Illumina, Inc., San Diego, CA 92122 USA.
authors.forename: Marina
authors.initials: M
authors.lastname: Bibikova
authors.affiliation: Illumina, Inc., San Diego, CA 92122 USA.
authors.forename: Brandy
authors.initials: B
authors.lastname: Klotzle
authors.affiliation: The University of Chicago, Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, Chicago, IL 60637, USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Glenn-Pratola
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Schell
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: Ronald L
authors.initials: RL
authors.lastname: Coleman
authors.affiliation: Genea Biocells, Sydney, New South Wales 2000, Australia.
authors.forename: Mauricio C
authors.initials: MC
authors.lastname: Cabral-da-Silva
authors.affiliation: Genea Biocells, Sydney, New South Wales 2000, Australia.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schmidt
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: Peterson
authors.affiliation: The University of Chicago, Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, Chicago, IL 60637, USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.affiliation: The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA. Electronic address: jloring@scripps.edu.
authors.forename: Jeanne F
authors.initials: JF
authors.lastname: Loring
authors.affiliation: Illumina, Inc., San Diego, CA 92122 USA. Electronic address: JFan@illumina.com.
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism* / Q000031:analogs & derivatives; D002454:Cell Differentiation; D002478:Cells, Cultured; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D006801:Humans; D008969:Molecular Sequence Data; D032386:Myoblasts, Cardiac / Q000378:metabolism; D058953:Neural Stem Cells; D039904:Pluripotent Stem Cells / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
keywords: 5-hydroxymethylcytosine; Cardiovascular cells; DNA methylation; Differentiation; Epigenetics; Human pluripotent stem cells; Neuronal cells; TAB-array