1. RPKM M1DPIF1DPIM6DPIF6DPIM1DPIF1DPIM6DPIF6DPI SenseAntisense Fig. S1 Boxplot showing distribution of RPKM of all TAIR10 protein-coding genes (sense) and their antisense transcripts in four samples investigated in this study. The highest expression level in F6DPI was observed in disease resistance gene At5g44420 (plant defensin 1.2). Supporting Information Figs S1-S2, S4-S5

2. Fig. S2 Read density across the region containing At1g13607, At1g13608 and At1g13609, and exon-exon junction reads from transcripts antisense to At1g13609. At1g13607 At1g13608 At1g13609.1 At1g13609.2 Forward strand Reverse strand RNA-seq reads across exons

3. Read density of the reverse strand 15 69 5 398 Read density of the forward strand M1DPI F1DPI M6DPI F6DPI M1DPI 65 F1DPI M6DPI F6DPI 2 12 TAR-83TAR-82TAR-66TAR-67 At1g47395At1g47400 At1g47405 0 Fig. S4 Expression level of transcriptionally active regions (TARs) in RNAi lines. For each TAR, the expression level in M1DPI was set to 1. Error bars represent standard deviations. ** denotes significant difference at p<0.01 (t-test). Fig. S5 The genomic organization and read densities of the co-induced features in a ~10kb region. ** Relative expression level