Figure 6.

TDP-43 shows distinct condensation-dependent binding, and CR mutants have defects in autoregulation

(A) Mapping of TDP-43 iCLIP data onto Malat1 non-coding RNA. Two replicates were summed, and iCLIP data were normalized and converted into smoothed lines using the rollmean function with a window size of 20 and mapped to a 250-nt-long regions on the ncRNA Malat1 (hg38 chr11:65501021-65501271:+) with CR-independent binding behavior. A crosslinking signal derived from the following two different iCLIP experiments is shown. Top panel: CR mutant TDP-43 variants. Center panel: hnRNPA2 constructs as described in Figure 4F. Bottom panel: the assigned binding regions colored according to their motif bias: YG-, YA-, and AA-containing [UG]n in green, blue, and red, respectively.

(B) As in (A) for a CR-dependent and 1,6-HD-sensitive binding region on a 400-nt-long region of the ncRNA Malat1 (hg38 chr11:65504300-65504700:+).

(C) As in (A) for a CR-dependent and 1,6-HD-sensitive region in the 3′ UTR of the endogenous TARDBP RNA (hg38 chr1:11023414-11023698:+).

(D) Quantification of the western blot analysis of the endogenous TDP-43 levels after 2 days of induction of each of the GFP-TDP-43 variants; see the corresponding western blot in Figure S6B. Statistical significance of n = 3 was calculated using Student’s t test with ^∗p < 0.05, ^∗∗p < 0.01.