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. 2017 Mar 21;114(14):E2965–E2974. doi: 10.1073/pnas.1618834114

Fig. 2.

Fig. 2.

CPD mapping and overlap with canonical, 21-, 22-, and 24-nt siRNAs. (A) Design of the experiment. Three-week-old plants (n = 12/replicate), grown in soil, were used in two independent biological replicates for untreated plants and four independent biological replicates for UV-C-treated plants. The sRNA and DNA were prepared from the pool of tissue for each replicate and subsequently used for sRNA sequencing and IPOUD + DNA sequencing. CPDs are displayed in yellow triangles. (B) Visualization of genome-wide CPDs distribution (black bar) on Arabidopsis chromosomes using Circos representation. The outermost circle displays the five Arabidopsis chromosomes. The inner circles represent the genome-wide CPDs distribution for each replicate of untreated and UV-C-treated samples (rainbow colors). The inner circle represents the siRNAs (21, 22, and 24 nt) overlapping CPD-damaged loci. The height of the histogram bins indicates siRNA abundance. (C) Histogram representing the origins (intergenic, TE, and protein-coding genes) of CPD-containing loci for each replicate of untreated (no UV-C) and UV-C-treated samples. The Arabidopsis thaliana genome (At) was used as a reference. Chi2 test: *P < 0.05. (D) Independent confirmation of hot spots using IPOUD-qPCR. Histogram (±SD) representing the enrichment of CPDs (IP/input) at hot spots overlapping with intergenic regions, protein-coding genes, and other types of regions excluding TEs (Others). Two biological replicates of untreated and three biological replicates of UV-C-treated in vitro-grown plants were used. Numbers indicate the hot spot sequence name. Actin 2 was used as negative control. (E) Pie chart representing the origins of hot spots of CPDs containing loci. (F) Histogram representing the origins of CPD containing loci mapping with 21-, 22-, and 24-nt siRNAs for each replicate of untreated (no UV-C) and UV-C-treated samples. Chi2 test: *P < 0.05 compared with untreated samples. (G) Box plots representing the abundance of 21-, 22-, and 24-nt siRNAs mapping to intergenic regions enriched in CPDs. Mann−Whitney U test *P < 0.05, ns, nonsignificant.