DNA methylation models

About

Together with the group of Jörn Walter we develop stochastic models that describe epigenetic modifications of the DNA. We focus on methyl groups that are attached to CpG dyads with the help of DNMTs. Epigenetic modifications such as DNA methylation play an important role in the understanding of embryogenesis. Moreover, changes in epigenetic factors can play a critical role in certain diseases. We use Markov models to describe the methylation activities of the DNMTs and the loss of methylation due to DNA replication. Our most recent models were able to make accurate predictions of the methylation frequencies.

Publications

  • J. Arand, D. Spieler, T. Karius, M. R. Branco, D. Meilinger, A. Meissner, T. Jenuwein, G. Xu, H. Leonhardt, V. Wolf, J. Walter: In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases, PLOS Genetics, 2012.
  • C. Kyriakopoulos, P. Giehr, G. Fisz, V. Wolf, J. Walter: The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: a HMM approach, PLoS Computational Biology, 2016
  • M. A. Eckersley-Maslin, V. Svensson, C. Krüger, T. Stubbs, P. Giehr, F. Krüger, R. Miragaia, C. Kyriakopoulos, R. Berrens, I. Milagre, J. Walter, S. Teichmann, W. Reik: MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs, Cell Reports, 2016
  • C. Kyriakopoulos, P. Giehr, V. Wolf: H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data, Bioinformatics, 2017
  • A. Lück, P. Giehr, J. Walter, V. Wolf: A Stochastic Model for the Formation of Spatial Methylation Patterns, CMSB 2017.
  • P. Giehr, C. Kyriakopoulos, K. Lepikhov, S. Walner, V. Wolf, J. Walter: Two are better than one: HPoxBS – Hairpin oxidative Bisulfite Sequencing, Nucleic Acids Research, 2018
  • C. Kyriakopoulos, P. Giehr, A. Lück, J. Walter, V. Wolf: A Hybrid HMM Approach for the Dynamics of DNA Methylation, HSB 2019
  • C. Kyriakopoulos, P. Giehr, K. Nordström, S. Abdulrahman, F. Müller, F. von Meyenn, G. Ficz, W. Reik, V. Wolf, J. Walter: Genome-wide single-base resolution efficiency profiling reveals modulation of maintenance and de novo methylation by Tet di-oxygenases, under review