Genome-wide profilings of EDM2-mediated effects on H3K9me2 and transcripts in Arabidopsis thaliana

EDM2 is a PHD finger-containing histone binding protein in Arabidopsis thaliana (Arabidopsis) that affects levels of the transposon silencing mark H3K9me2. Here we report on genome-wide profiling by ChIP-seq and RNA-seq of EDM2-mediated effects on H3K9me2 and rRNA-depleted transcripts, respectively. EDM2 affects H3K9me2 and/or transcript levels at hundreds transposons and over 3000 gene loci including 60 NLR genes. In addition, EDM2 also binds to several NLR genes and transposons. Overall design: H3K9me2 ChIP-seq and rRNA depletion expression profiling in edm2 and wild-type (WT) Col-0; EDM2 binding site identificaion by HA-tagged ChIP-seq for E2pro:HA-E2c line and Col-0