ChIP-seq Analysis of Histone Modifications

The ChIP-seq assay was performed according to a published protocol [31 (link)]. Two commercial antibodies, H3K27me3 (Sigma, Cat. #07–449) and H3K27ac (Sigma, Cat. #07–360), were used for immunoprecipitation. The ChIP DNAs were ligated with Illumina sequencing adaptors and sequenced using the Illumina HiSeq platform to produce 150 bp paired-end reads. The raw reads generated from ChIP-seq were quality filtered and trimmed using trim_galore. Cleaned reads were mapped to the B. distachyon genome using Bowtie2 v.2.2.5 [50 (link)] with default parameters. Mapped reads were filtered using SAMtools v.1.9 [51 (link)] to retain only correctly read pairs with a mapping quality score ≥ 10 for further analysis. Peak calling was performed using MACS2 v.2.1.4 [52 (link)] with the parameters “-f BAMPE –broad -g 2.7e8 –nomodel”.