The Puf5p subnetwork was identified via RNA Tagging. (A) Plot of the fraction of Puf5p targets and all yeast mRNAs (all mRNAs) with the indicated PBE. (B) Pie chart illustrating the number of Puf5p targets with both a 9BE and 10BE (light gray), or either a 9BE or 10BE (dark gray) in their 3′ UTR. (C) Heat map displaying results of the k-means clustering analysis of all 916 Puf5p targets. Each row represents a single Puf5p target. Columns refer to the length of the U-tag detected on reads for each gene, from at least one uridine (leftmost column) to at least eight uridines (rightmost). Puf5p target classes are indicated (I, II, III, and IV). (D) Plot showing the enrichment of each class of Puf5p targets relative to all yeast mRNAs (all mRNAs) for 9BEs and 10BEs. (E) Schematic of wild-type (WT) and a mutant PHD1 mRNA that lacks its PBEs (ΔPBE), and a plot of the number of U-tagged mRNAs detected for WT and ΔPBE PHD1 mRNAs.
