Fig. 5: RNAPII stalling coincides with regulated termination near Arabidopsis promoters.

a Wild-type pNET-seq (8WG16)⁴³ coverage averaged around sppRNA PAS genomic positions for sppRNAs genes (n = 1155). b Genome browser screenshot of wild-type pNET-seq reads at the MPK20 gene. TIF-cluster diagram indicates annotates mRNA and sppRNA transcript isoforms. Red arrow indicates sppRNAs TIF-cluster. c Wild-type pNET-seq (8WG16)⁴³ coverage averaged around sppRNA PAS genomic positions for sppRNAs genes (n = 1155) and a control set of genes displaying equal distribution of nascent gene body transcription (n = 1153). Inset violin plot depicts significantly increased average pNET-seq signal within first 150 nt from TSS for genes with sppRNAs (Wilcoxon test: p < 2.2e−16) compared to the control genes. Shading in a and c represents the calculated confidence interval on the mean of 95%. d Heatmap of cis-element GAGA-box (GAGAR) in genomic regions 200 bp upstream and 150 bp downstream of the TSS of control genes with equal pNET-seq nascent transcription distribution to sppRNA genes (n = 1155). e Violin plot of the average GAGAR density downstream of the TSS (two-sided Wilcoxon test: p < 2.2e−16). f Heatmap of cis-element TCP-binding motif (RGCCCAW) in genomic regions 200 bp upstream and 150 bp downstream of the TSS of control genes with equal pNET-seq nascent transcription distribution to sppRNA genes (n = 1155). The colour scale in d and f represents motif frequency from low (white) to high (red). g Violin plot of the average GAGAR density upstream of the TSS (two-sided Wilcoxon test: p < 2.2e−16). The inset box in c and boxes in e and g bounds the iQR divided by the median, and whiskers extend to a maximum of 1.5× iQR beyond the box.