A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes

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 …

@article{kyriakopoulosAComprehensiveApproachFor2022,
 author = {Charalampos Kyriakopoulos and Karl Nordström and Paula Linh Kramer and Judith Yumiko Gottfreund and Abdulrahman Salhab and Julia Arand and Fabian Müller and Ferdinand von Meyenn and Gabriella Ficz and Wolf Reik and Verena Wolf and Jörn Walter and Pascal Giehr},
 doi = {10.1016/j.crmeth.2022.100187},
 journal = {Cell Reports Methods},
 month = {3},
 number = {3},
 pages = {1-23},
 publisher = {Cell Press},
 title = {A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes},
 volume = {2},
 year = {2022}
}