Acute Depletion Redefines the Division of Labor among DNA Methyltransferases in Methylating the Human Genome
Rochelle L. Tiedemann,
Emily L. Putiri,
Jeong-Heon Lee,
Ryan A. Hlady,
Katsunobu Kashiwagi,
Tamas Ordog,
Zhiguo Zhang,
Chen Liu,
Jeong-Hyeon Choi,
Keith D. Robertson
Affiliations
Rochelle L. Tiedemann
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Emily L. Putiri
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Jeong-Heon Lee
Department of Biochemistry and Molecular Biology, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Ryan A. Hlady
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Katsunobu Kashiwagi
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Tamas Ordog
Department of Physiology and Biomedical Engineering, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Zhiguo Zhang
Department of Biochemistry and Molecular Biology, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Chen Liu
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, P.O. Box 100275, Gainesville, FL 32610, USA
Jeong-Hyeon Choi
Cancer Center, Georgia Regents University, 1411 Laney Walker Boulevard, Augusta, GA 30912, USA
Keith D. Robertson
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
Global patterns of DNA methylation, mediated by the DNA methyltransferases (DNMTs), are disrupted in all cancers by mechanisms that remain largely unknown, hampering their development as therapeutic targets. Combinatorial acute depletion of all DNMTs in a pluripotent human tumor cell line, followed by epigenome and transcriptome analysis, revealed DNMT functions in fine detail. DNMT3B occupancy regulates methylation during differentiation, whereas an unexpected interplay was discovered in which DNMT1 and DNMT3B antithetically regulate methylation and hydroxymethylation in gene bodies, a finding confirmed in other cell types. DNMT3B mediated non-CpG methylation, whereas DNMT3L influenced the activity of DNMT3B toward non-CpG versus CpG site methylation. Altogether, these data reveal functional targets of each DNMT, suggesting that isoform selective inhibition would be therapeutically advantageous.
