title: Modeling DNA methylation dynamics with approaches from phylogenetics.
abstract: BACKGROUND
  Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates. Genome-wide DNA methylation assays have become increasingly common, and this has enabled characterization of DNA methylation in distinct stages across differentiating cellular lineages. Changes in CpG methylation are essential to cellular differentiation; however, current methods for modeling methylation dynamics do not account for the dependency structure between precursor and dependent cell types.
  
  
  RESULTS
  We developed a continuous-time Markov chain approach, based on the observation that changes in methylation state over tissue differentiation can be modeled similarly to DNA nucleotide changes over evolutionary time. This model explicitly takes precursor to descendant relationships into account and enables inference of CpG methylation dynamics. To illustrate our method, we analyzed a high-resolution methylation map of the differentiation of mouse stem cells into several blood cell types. Our model can successfully infer unobserved CpG methylation states from observations at the same sites in related cell types (90% correct), and this approach more accurately reconstructs missing data than imputation based on neighboring CpGs (84% correct). Additionally, the single CpG resolution of our methylation dynamics estimates enabled us to show that DNA sequence context of CpG sites is informative about methylation dynamics across tissue differentiation. Finally, we identified genomic regions with clusters of highly dynamic CpGs and present a likely functional example. Our work establishes a framework for inference and modeling that is well suited to DNA methylation data, and our success suggests that other methods for analyzing DNA nucleotide substitutions will also translate to the modeling of epigenetic phenomena.
  
  
  METHODS
  Source code is available at www.kostkalab.net/software.
authors.affiliation: Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Capra
authors.affiliation: Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, Departments of Developmental Biology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA 15201, USA.
authors.forename: Dennis
authors.initials: D
authors.lastname: Kostka
mesh_terms: D000818:Animals; D001483:Base Sequence; D002454:Cell Differentiation / Q000235:genetics; D018899:CpG Islands; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D023281:Genomics; D008390:Markov Chains; D051379:Mice; D008957:Models, Genetic; D010802:Phylogeny
chemical_list: D004247:DNA