A Stochastic Model for the Formation of Spatial Methylation Patterns

DOI10.1007/978-3-319-67471-1_10zbMATH Open1416.92062arXiv1706.10145OpenAlexW2962727706MaRDI QIDQ5227327FDOQ5227327

Verena Wolf, Jörn Walter, Alexander Lück, Pascal Giehr

Publication date: 25 July 2019

Published in: Computational Methods in Systems Biology (Search for Journal in Brave)

Abstract: DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood and recently different mechanistic models of enzyme activities responsible for DNA methylation have been proposed. Here we extend existing Hidden Markov Models (HMMs) for DNA methylation by describing the occurrence of spatial methylation patterns over time and propose several models with different neighborhood dependencies. We perform numerical analysis of the HMMs applied to bisulfite sequencing measurements and accurately predict wild-type data. In addition, we find evidence that the enzymes' activities depend on the left 5' neighborhood but not on the right 3' neighborhood.

Full work available at URL: https://arxiv.org/abs/1706.10145

zbMATH Keywords

DNA methylationhidden Markov modelspatial stochastic model

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Applications of stochastic analysis (to PDEs, etc.) (60H30)

Cited In (3)

• Physical modeling of the spreading of epigenetic modifications through transient DNA looping
• A Stochastic Automata Network Description for Spatial DNA-Methylation Models
• Modeling dependence in methylation patterns with application to ovarian carcinomas

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