Skip to main content
Figure 3 | BMC Genomics

Figure 3

From: Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data

Figure 3

Position-specific enrichment of uncapped 5′-ends surrounding putative PUF binding sites. Distribution of normalized reads around putative PUF binding sites in the 3′ UTR of Arabidopsis genes with deep sequencing data derived from the PARE method (A), degradome sequencing (C), and GMUCT method (D) and rice (B), soybean (E) and yeast (F) genes with PARE data. Motifs were boxed and the first nucleotide of motifs was set as 1. Loci containing the motif of interest were identified from the 3′ UTR of all annotated genes and the number is shown in parentheses above the heat map. For Arabidopsis and rice, only loci with a total read number greater than five in the 20-nt region are shown and the number of loci in each heat map is also indicated above the heat map. Loci were clustered based on the distribution of normalized read numbers across the 20-nt region by Ward’s method. Uncapped 5′-ends associated with putative PUF binding sites in Arabidopsis (G) and rice (H) were independently validated by the modified 5′ RACE protocol. The frequency of uncapped 5′-ends among clones sequenced at the position corresponding to the dominant termini supported by deep sequencing data is indicated with a filled arrow whereas at other positions it is indicated with an open arrow. Putative PUF binding sites are boxed.

Back to article page