FIGURE 3.

Noncoding and repeat RNA analysis reveals novel PCBP2–RNA interactions. (A,B) Coverage histogram of PCBP2 or hnRNP-C (respectively) iCLIP reads mapping to the 42-kb human rDNA locus. Total reads mapping to the rDNA were used to calculate a fraction of total per RT stop and binding sites are reported as such. The mature sequences of the 18S, 5.8S, and 28S rRNAs are highlighted in gray. (C) PCBP2 iCLIP reads mapping to snoRNA loci were tallied and plotted as percentages mapping to the three snoRNA classes; C/D box, H/ACA box, and scaRNAs (center). Reads mapping to C/D box or H/ACA box snoRNAs were extracted and plotted across a normalized snoRNA transcript of 100 units long and read percentages were calculated as in left and right bar plots, respectively. (D) PCBP2 iCLIP reads mapping to the Y RNA 1 (left) and Y RNA 3 (right) transcripts are plotted as in (A). Secondary structure predictions of each RNA were produced with mFold and nucleotides identified as having PCBP2 iCLIP RT stops are highlighted in red.