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Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Kartal Önder, Schmid Marc W., Grossniklaus Ueli,
Project The Genetic and Molecular Basis of Gametogenesis and Maternal Effects in Arabidopsis
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Original article (peer-reviewed)

Journal Genome Biology
Volume (Issue) 21(1)
Page(s) 172 - 172
Title of proceedings Genome Biology
DOI 10.1186/s13059-020-02068-2

Open Access

URL http://doi.org/10.1186/s13059-020-02068-2
Type of Open Access Publisher (Gold Open Access)

Abstract

In population genomics, genetic diversity measures play an important role in genome scans for divergent sites. In population epigenomics, comparable tools are rare although the epigenome can vary at several levels of organization. We propose a model-free, information-theoretic approach, the Jensen-Shannon divergence (JSD), as a flexible diversity index for epigenomic diversity. Here, we demonstrate how JSD uncovers the relationship between genomic features and cell type-specific methylome diversity in Arabidopsis thaliana. However, JSD is applicable to any epigenetic mark and any collection of individuals, tissues, or cells, for example to assess the heterogeneity in healthy organs and tumors.
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