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Kyriakopoulos C, Nordström K, Kramer PL, Gottfreund JY, Salhab A, Arand J, Müller F, von Meyenn F, Ficz G, Reik W, Wolf V, Walter J, Giehr P. A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes. Cell Rep Methods 2022; 2:100187. [PMID: 35475220 PMCID: PMC9017147 DOI: 10.1016/j.crmeth.2022.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/19/2022] [Accepted: 03/01/2022] [Indexed: 10/25/2022]
Abstract
A precise understanding of DNA methylation dynamics is of great importance for a variety of biological processes including cellular reprogramming and differentiation. To date, complex integration of multiple and distinct genome-wide datasets is required to realize this task. We present GwEEP (genome-wide epigenetic efficiency profiling) a versatile approach to infer dynamic efficiencies of DNA modifying enzymes. GwEEP relies on genome-wide hairpin datasets, which are translated by a hidden Markov model into quantitative enzyme efficiencies with reported confidence around the estimates. GwEEP predicts de novo and maintenance methylation efficiencies of Dnmts and furthermore the hydroxylation efficiency of Tets. Its design also allows capturing further oxidation processes given available data. We show that GwEEP predicts accurately the epigenetic changes of ESCs following a Serum-to-2i shift and applied to Tet TKO cells confirms the hypothesized mutual interference between Dnmts and Tets.
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Affiliation(s)
| | - Karl Nordström
- Department of Genetics and Epigenetics, Saarland University, Campus A2.4, 66123 Saarbrücken, Germany
| | - Paula Linh Kramer
- Computer Science Department, Saarland University, Campus E1.3, 66123 Saarbrücken, Germany
| | - Judith Yumiko Gottfreund
- Department of Genetics and Epigenetics, Saarland University, Campus A2.4, 66123 Saarbrücken, Germany
| | - Abdulrahman Salhab
- Department of Genetics and Epigenetics, Saarland University, Campus A2.4, 66123 Saarbrücken, Germany
| | - Julia Arand
- Division of Cell and Developmental Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Fabian Müller
- Department of Integrative Cellular Biology and Bioinformatics, Campus A2.4, 66123 Saarbrücken, Germany
| | - Ferdinand von Meyenn
- Department of Health Sciences and Technology, ETH Zürich, Schorenstrasse 16, Schwerzenbach, 8603 Zürich, Switzerland
| | - Gabriella Ficz
- Haemato-Oncology, Queen Mary University of London, London EC1M 6BQ, UK
| | - Wolf Reik
- Epigenetics Department, Babraham Institute, Cambridge CB22 3AT, UK
| | - Verena Wolf
- Computer Science Department, Saarland University, Campus E1.3, 66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Campus A2.4, 66123 Saarbrücken, Germany
| | - Pascal Giehr
- Department of Genetics and Epigenetics, Saarland University, Campus A2.4, 66123 Saarbrücken, Germany
- Department of Health Sciences and Technology, ETH Zürich, Schorenstrasse 16, Schwerzenbach, 8603 Zürich, Switzerland
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