title: Quantitative LC-MS Provides No Evidence for m6dA or m4dC in the Genome of Mouse Embryonic Stem Cells and Tissues.
abstract: Until recently, it was believed that the genomes of higher organisms contain, in addition to the four canonical DNA bases, only 5-methyl-dC (m5dC) as a modified base to control epigenetic processes. In recent years, this view has changed dramatically with the discovery of 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC) in DNA from stem cells and brain tissue. N6-methyldeoxyadenosine (m6dA) is the most recent base reported to be present in the genome of various eukaryotic organisms. This base, together with N4-methyldeoxycytidine (m4dC), was first reported to be a component of bacterial genomes. In this work, we investigated the levels and distribution of these potentially epigenetically relevant DNA bases by using a novel ultrasensitive UHPLC-MS method. We further report quantitative data for m5dC, hmdC, fdC, and cadC, but we were unable to detect either m4dC or m6dA in DNA isolated from mouse embryonic stem cells or brain and liver tissue, which calls into question their epigenetic relevance.
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Schiffers
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Ebert
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: René
authors.initials: R
authors.lastname: Rahimoff
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Olesea
authors.initials: O
authors.lastname: Kosmatchev
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Jessica
authors.initials: J
authors.lastname: Steinbacher
authors.affiliation: Biocenter of the LMU, Dept. Biologie 1 - Botanik, Molekulare Pflanzenwissenschaften, Grosshaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany.
authors.forename: Alexandra-Viola
authors.identifier: 0000-0001-9638-0762
authors.initials: AV
authors.lastname: Bohne
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Fabio
authors.identifier: 0000-0002-7148-9013
authors.initials: F
authors.lastname: Spada
authors.affiliation: CiPSM, Department of Pharmacy, LMU München, Pharmacology for Life Sciences, Butenandtstr. 7, 81377, München, Germany.
authors.forename: Stylianos
authors.identifier: 0000-0001-5092-9238
authors.initials: S
authors.lastname: Michalakis
authors.affiliation: Biocenter of the LMU, Dept. Biologie 1 - Botanik, Molekulare Pflanzenwissenschaften, Grosshaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany.
authors.forename: Jörg
authors.identifier: 0000-0003-4184-4560
authors.initials: J
authors.lastname: Nickelsen
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Markus
authors.identifier: 0000-0002-3579-3317
authors.initials: M
authors.lastname: Müller
authors.affiliation: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany.
authors.forename: Thomas
authors.identifier: 0000-0001-7898-2831
authors.initials: T
authors.lastname: Carell
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D016825:Chlamydomonas reinhardtii / Q000235:genetics; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D003562:Cytidine / Q000031:analogs & derivatives* / Q000378:metabolism*; D004247:DNA / Q000235:genetics; D044127:Epigenesis, Genetic; D016678:Genome; D057230:Limit of Detection; D008099:Liver / Q000378:metabolism*; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism*; D046939:Synechocystis / Q000235:genetics
chemical_list: D003562:Cytidine; D004247:DNA
keywords: DNA; epigenetics; mass spectrometry; methyldeoxyadenosine; methyldeoxycytidine