Figure 1. HITS-CLIP Identifies MBNL2-RNA^exp Interactions in DM Brain.

(A) Strategy for identifying RBP-RNA^exp binding interactions using HITS-CLIP. For DM1, a CTG repeat (red box) in the DMPK 3′UTR (coding exons, thick black boxes; UTRs, thin black boxes; introns, thin lines) expands in disease (CUG^exp, red triangle). Upon transcription, the mRNA (grey) forms a stem-loop that sequesters MBNL2 (blue ovals). HITS-CLIP of MBNL proteins using DM1 (right), but not control (left), tissue generates a large increase in reads clustered over the repeat region (bottom right).

(B) MBNL2 binding profile reveals enriched binding to the DMPK CTG^exp in DM1 brain. UCSC browser view showing wiggle plots of MBNL2 HITS-CLIP binding in the DMPK reference gene for control (orange), DM1 (green), and DM2 (blue) human hippocampus. Zoomed-in view of the terminal exon (bottom right) showing a clustered read peak over the CTG repeat region for DM1 only. Quantification (bottom left) of MBNL2 CLIP peak read depth (RPKM) over the DMPK CTG repeat region shows a significant enrichment (36-fold) over controls (n = 3 per group, data are reported ± SEM, *p < 0.05).

(C) MBNL2 HITS-CLIP binding profile for CNBP. Intron 1 (bottom right) containing the CCTG repeat region (red box) is shown. Quantification (bottom left) of average peak read depth over CCTG repeats showing a 79-fold enrichment in DM2 over controls (n = 3 per group, data are reported ± SEM, ***p < 0.001).