Fig. 1

Identification of potential direct POLV and JMJ14 target genes. a Bioinformatics pipeline used for identifying targets. Transcriptome (RNAseq) data from mutant (polv, jmj14) and wild-type (WT) infected plants were processed separately at 4 and 7 days post-inoculation (dpi). Differential expression analysis was performed for each dpi using mutant infected samples as treatment and WT as control (mutant-enhanced infected group analysis). The genomic locations of all mutant-enhanced genes that were induced at 4 or 7 dpi, including 1 kilobase (kb) upstream of their transcriptional start sites (TSS), were extracted and overlapped with chromatin immunoprecipitation data (ChIP-seq). The genomic ranges of the POLV-regulated genes were compared to the combined chromatin occupancy of the RdDM-related proteins POLIV, POLV, DRD1, DMS3, RDM1 and H3K9m2 obtained from the NCBI GEO database. For the JMJ14-regulated set, genic locations were overlapped with JMJ14 ChIP-seq peaks and regions found to gain H3K4m3 marks in jmj14 mutants when compared to WT plants. b The total number of differentially expressed genes (DEGs) discovered in the mutant-enhanced infected group prior to filtering with ChIP-seq data (adjusted P = 0.05). For each condition, three biological replicates were used, each with a pool of 12 plants. c Venn diagram depicting the total number of DEGs induced in the mutant-enhanced infected group with significant overlaps with ChIP-seq data