Figure 7. IDR-dependent binding of ECT2 to U-rich motifs 5’ of m⁶A.

(A) Top panels: Distance-based enrichment of motifs at and around m⁶A-Nanopore (Np, Parker et al., 2020) sites, plotted as motif counts per 1000 m⁶A sites (purple lines). Gray lines indicate the enrichment in a location-matched background set as in Figure 5D. Middle and bottom panels: sites are split according to whether they sit on ECT2 targets (middle), or to distance from the nearest ECT2 crosslink site (for ECT2-iCLIP targets only) (bottom). Additional motifs are shown in the Figure 7—figure supplement 1. (B) Cartoon illustrating the ECT2 IDR RNA-binding and competition hypotheses. (C) Normalized density of ECT2 iCLIP crosslink sites identified in the libraries corresponding to the 110- and 55-kDa bands (Figure 3B) at and up to +/-200 nt of m⁶A-Nanopore sites. (D) Motifs per 1000 ECT2-iCLIP crosslink sites (CS) split according to whether they are found in libraries from both 110-kDa and 55-kDa bands (IDR-independent’), or exclusively (distance > 10 nt) in the 110-kDa band (’IDR-dependent’). Gray lines indicate the enrichment in a location-matched background set as in Figure 5D. Additional motifs are shown in Figure 7—figure supplement 2 and Supplementary file 3.

Figure 7—figure supplement 1. Motif preferences around m⁶A sites according to ECT2 binding.

From top to bottom: (1) motif logos for derived position weight matrices (PWMs); (2) distance-based enrichment of motifs at and around m⁶A-Nanopore* sites, plotted as motif counts per 1000 m⁶A sites (purple lines). Gray lines indicate the enrichment in a location-matched background set as in Figure 5D; (3) same as in (2) with sites split according to whether they sit on ECT2 targets; (4) same as in (2) with sites split according to the distance from the nearest ECT2 crosslink site (for ECT2-iCLIP targets only); (5) motif counts per 1000 iCLIP-binding sites, as a function of distance from the iCLIP position, showing all sites against matched background sites (gray lines). Motifs are ordered according to the different relative enrichment upstream or downstream m⁶A sites according to ECT2 binding (see text below panels 3 and 4). * Parker et al., 2020.

Figure 7—figure supplement 2. Dependency of the ECT2 intrinsically disordered region (IDR) for motif enrichment.

(A) Proportion of ECT2-iCLIP sites at each nucleotide for the 110kDa and 55kDa bands. (B) From top to bottom: (1) motif logos for derived position weight matrices (PWMs); (2) distribution of motifs per 1000 ECT2-iCLIP crosslink sites (red) or matched-locations background (gray), ±75 nt of the site; (3) motifs per 1000 ECT2-iCLIP crosslink sites, split according to whether they are found in libraries from both 110kDa and 55kDa bands (’IDR-independent’) or exclusively (distance >10 nt) in the 110kDa band (’IDR-dependent’).