Fig. 6: SPT6L is required to maintain Pol V transcripts.

a Genome tracks display the ChIP-seq and RIP-seq signals on chromosome 5. The RIP-seq signals of each sample from different strands were displayed as positive and negative values. The signals from nrpe1 RIP-seq sample were serves as background. The black arrows pointed to the loci with changed NRPE1 RIP signals in spt6l. The ChIP-seq or RIP-seq signals of each sample were averaged over two biological replicates. b Boxplots showed the amount of Pol V transcripts in NRPE1-GFP and spt6l NRPE1-GFP within Pol V peaks. The reads number were normalized to total mapped RIP-seq reads of each sample. Unpaired Wilcoxon test was performed. P < 2.2e⁻¹⁶. Two biological replicates were included. c Profiles of normalized NRPE1 RIP-seq reads from NRPE1-GFP and spt6l NRPE1-GFP within four previous defined genomic groups (Fig. 1c). Two biological replicates were included. d Boxplots showed the reads length of NRPE1 RIP-seq from NRPE1-GFP and spt6l NRPE1-GFP. Unpaired Wilcoxon test was performed. P < 2.2e⁻¹⁶. Two biological replicates were included. e The Ratio of reads containing uridine (U) at position 10 (U-10 reads) in different Pol V peak groups. The Pol V peaks were divided into four groups base on the ratio of U-10 GRO-seq reads in each Pol V peaks (see Bioinformatic analysis). The ratio of U-10 reads generated from GRO-seq (SRR5681049 and SRR5681053), NRPE1 RIP, spt6l NRPE1 RIP, and Random reads were plotted. The plotted values are averaged over two biological replicates (Random sample was averaged over three random shuffles). The center line of boxplot, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range.