Figure 1

PUM1 and PUM2 have distinct and similar binding characteristics. (A) Number of transcripts with 3′UTRs bound by PUM1 (light blue), PUM2 (dark blue), or both (black). Motif logos at the bottom depict the top-scoring enriched motif identified by DREME for the PUM1 and PUM2 sites, consistent with the previously determined PUM motif. (B) Cumulative distribution plot of mRNA level log fold change upon PUM knockdown⁵² for populations of transcripts with 3′UTRs bound by PUM1 (light blue), PUM2 (dark blue), both (black), or neither (gray). p-values correspond to a Kolmogorov-Smirnov test of each transcript set against the rest of the transcriptome. (C) Density of PUM motifs near PUM1 (light blue), PUM2 (dark blue), or overlapping (black) PUM sites. The shaded area represents a mean +/− 1 SD interval of 100 control densities where PUM motif locations were randomized within each 3′UTR, and distances to PUM2-only peaks computed. (D) DREME differential motif enrichment between PUM2 and PUM1 bound sequences show an enrichment of miRNA seed complements within the PUM2 sites.