期刊
CELL REPORTS METHODS
卷 2, 期 3, 页码 -出版社
CELL PRESS
DOI: 10.1016/j.crmeth.2022.100187
关键词
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资金
- DFG [SFB1309, 325871075]
- German Epigenome Programme (DEEP) of the Federal Ministry of Education and Research in Germany (BMBF) [01KU1216]
- German Federal Mindsistry of Research and Education grant [031L0101D]
GwEEP is a versatile approach that uses genome-wide hairpin datasets to infer dynamic efficiencies of DNA modifying enzymes, accurately predicting epigenetic changes in the genome.
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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