Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis
Figure 3
Novel smRNA–producing substrates of RDR6.
(A–D) Four examples of RDR6 smRNA-generating substrates identified using the combination of dsRNA- and smRNA-seq (screenshots from http://tesla.pcbi.upenn.edu/annoj_at9/). W (green bars) and C (red bars) indicate sequence reads from Watson and Crick strands, respectively. (A) At5g39370 (previously identified), (B) At1g20370 (novel), (C) the intergenic region just upstream of At2g41490 (novel), and (D) At3g19890 (novel). (E) Random-primed RT-qPCR analysis of four previously identified and 10 novel RDR6 substrates for wild-type Col-0 and rdr6-11 mutant plants. Error bars, ±SD. ** indicates p-value <.001. Green and red lines underline previously identified and novel RDR6 substrates, respectively. * denotes RDR6 substrates that produce phased siRNAs.