Abstract
DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As is evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation, also control tissue-specific methylation patterns, with the most striking pattern observed in ovules where CLSY3 and CLSY4 control DNA methylation at loci with a highly conserved DNA motif. On a more global scale, we demonstrate that specific clsy mutants are sufficient to shift the epigenetic landscape between tissues. Together, these findings reveal substantial epigenetic diversity between tissues and assign these changes to specific CLSY proteins, elucidating how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.
Highlights
DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing
As a first step in determining whether the CLSYs play a role in shaping tissue-specific patterns of DNA methylation, their expression patterns were assessed during Arabidopsis development
Beyond confirming the tissue-specific expression patterns of the CLSYs, analysis of the mRNA-seq data revealed that these genes show the most diverse expression patterns when compared to the rest of the RNA-directed DNA methylation (RdDM) machinery, the main genes required for the maintenance of DNA methylation in the different sequence contexts, or the four demethylases (Fig. 1c)
Summary
DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. Several recent studies in Arabidopsis thaliana (Arabidopsis)[6,7,8,9,10], rice[11,12], Brassica rapa[13], and soybean[14] have compared the epigenomes of different somatic tissues and/or cell types All of these studies implicate the RdDM pathway in the establishment of specific DNA methylation patterns, including several[12,13] that describe a highly expressed set of 24nt-siRNA producing loci initially designated as siren (small-interfering RNA in endosperm) loci based on their tissue of discovery[12]. Much of our understanding of how DNA methylation is established and maintained stems from the characterization of proteins discovered using genetic and biochemical approaches These studies have revealed multiple interconnected methylation and demethylation pathways that provide a framework for understanding how different DNA methylation patterns are generated. These methylation and demethylation pathways constitute a dynamic system to control
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