Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts. Overall design: Examination of unopened flower bud small RNAs from wild type and various single or double mutant combinations, many of which have biological replicates. Small RNA sequences from wt Col, controls and other mutants shown in the study are available at GSE41755 and GSE57191.