Putting DNA methylation in context: from genomes to gene expression in plants

Abstract

Plant DNA methylation is its own language, interpreted by the cell to maintain silencing of transposons, facilitate chromatin structure, and to ensure proper expression of some genes. Just as in any language, context is important. Rather than being a simple “on-off switch”, DNA methylation has a range of “meanings” dependent upon the underlying sequence and its location in the genome. Differences in the sequence context of individual sites are established, maintained, and interpreted by differing molecular pathways. Varying patterns of methylation within genes and surrounding sequences are associated with a continuous range of expression differences, from silencing to constitutive expression. These often-subtle differences have been pieced together from years of effort, but have taken off with the advent of methods for assessing methylation across entire genomes. Recognizing these patterns and identifying underlying causes is essential for understanding the function of DNA methylation and its systems-wide contribution to a range of processes in plant genomes.

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

“…DNA methylation, occurring in three sequence contexts in plants (mCG, mCHG, and mCHH, where H is anything but G), is largely considered to function in transposable element (TE) silencing, maintaining genome stability, and possible regulation of gene expression (Reinders et al, 2009;Law and Jacobsen, 2010;Jones, 2012;Eichten et al, 2014;Niederhuth and Schmitz, 2017). This potential effect on gene expression has raised the proposition that DNA methylation could complement genetic variation, as a mode for transferring heritable information, to contribute to phenotypic variation (Molinier et al, 2006;Heard and Martienssen, 2014;Quadrana and Colot, 2016).…”

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

“…However, it recently became evident that DNA methylation appears to control the expression of only a small number of genes (Seymour and Becker 2017) and that the impact of DNA methylation on gene expression is distinctly influenced by other epigenetic modifications including histone modification and gene silencing by small noncoding RNA (Stroud et al 2014;Du et al 2015;Niederhuth and Schmidt 2017). Thus, to fully understand the function of DNA methylation in the embryogenic transition the functional outcome of DNA methylation in the context of other epigenetic changes remains to be uncovered.…”

Functional characterization of DEMETER-like DNA demethylases during growth-dormancy cycles in poplar

“…The role of gene body methylation is still unclear. In plants and animals, mCG in gene bodies has been associated with higher gene expression, and more specifically, with constitutively expressed genes (Niederhuth & Schmitz 2016). These genes showed reduced mCG in and around the TSS.…”

“…DNA methylation is mostly a repressive chromatin modification; however, this is not always the case (Niederhuth & Schmitz 2016). Methylation in the promoter affects transcription factor (TF) binding and, therefore, gene expression.…”

“…However, gene-body methylation in poplar has been correlated with tissue-specific expression and shows a more negative effect on transcription than promoter-gene methylation (Vining et al 2012;Lafon-Placette et al 2013). Generally methylation in CG of TSS is sufficient for transcriptional silencing (Niederhuth et al 2016). …”