MethEvolSIM - Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies
DNA methylation is an epigenetic modification involved in
genomic stability, gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl
group to cytosines, for example to cytosines in a CpG
dinucleotide context (CpG stands for a cytosine followed by a
guanine). Tissue-specific methylation patterns lead to genomic
regions with different characteristic methylation levels. E.g.
in vertebrates CpG islands (regions with high CpG content) that
are associated to promoter regions of expressed genes tend to
be unmethylated. 'MethEvolSIM' is a model-based simulation
software for the generation and modification of cytosine
methylation patterns along a given tree, which can be a
genealogy of cells within an organism, a coalescent tree of DNA
sequences sampled from a population, or a species tree. The
simulations are based on an extension of the model of Grosser &
Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for
changes of the methylation states at single cytosine positions
as well as simultaneous changes of methylation frequencies in
genomic structures like CpG islands.