Maize siRNAs are Associated with Euchromatin-like Environments that have High Accessibility and Relatively Low H3K9me2

RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNAi-related transcriptional gene silencing. To determine relationships between RdDM and heterochromatin in the repeat-rich maize genome, we carried out whole-genome analyses of several heterochromatic features: H3K9me2 and H3K27me2, chromatin accessibility, DNA methylation, and small RNAs, and we analyzed two mutants that affect these processes (mop1 and zmet2). The data reveal that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but which lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that siRNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.