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Genome-wide Discriminatory Information Patterns of Cytosine DNA Methylation
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1  University of Nebraska-Lincoln


Cytosine DNA methylation (CDM) is a highly abundant epigenetic heritable but reversible chemical modification to the genome. Herein, a machine learning approach, was applied to analyze the accumulation of epigenetic marks in 150 methylomes from Arabidopsis thaliana ecotypes. We hypothesize that these marks are chromosomal footprints that account for different ontogenetic and phylogenetic and histories of individual members of the sampling population. Our results support this hypothesis and suggest a statistical-physical relationship between CDM changes and single nucleotide polymorphism (SNPs). Furthermore, the genome-wide redistribution of CDM changes ensures the thermal stability of the DNA molecule preserving the integrity of the genetic message continuously stressed by thermal fluctuations in the cell environment.

Keywords: Epigenetics, Epigenomics, Information thermodynamics, Linear discriminant analysis, machine learning.
Comments on this paper
Georgia Tsiliki
LD patterns
Would it make sense to look at Linkage Disequilibrium patterns under these settings? and if yes, do you think the findings would be supplementary or perhaps overlapping with those presented here?

Robersy Sanchez
This a good question, since, in general, methylation changes at different loci are not necessarily independent. In particular, this happens in those loci where methylation is associated with gene expression, i.e., in loci where genes expression is regulated by cytosine DNA methylation at promoters or at gene-body. So, we would expect for those loci with Linkage Disequilibrium (LD), where methylation play a regulatory role, be associated in terms of methylation as well.
The results presented here indicate a general statistical tendencies that can support further studies on the relationship between LD and methylation.