Extended Data Fig. 11: Ku binds to monomeric Alu at the stem loops.
From: Ku limits RNA-induced innate immunity to allow Alu expansion in primates
a-b, The relative fraction of irAlu and non-irAlu defined by Wu et al. Cell 201867 bound by Ku (a) or DNA-PKcs (b). c, The distribution of LINE element orientation among the Ku and DNA-PKcs irCLIP sites. d-e, The irCLIP sites preference of Ku (d) and DNA-PKcs (e) in asAlu elements. The red is a higher frequency. f, The impact of irCLIP-Ku on mRNA expression. The Log2 (mean TPM + 1) in DMSO versus IAA-and Dox- treated (day 4) Ku80-AID samples were plotted. The red and blue dots are genes with irCLIP-Ku in 3′ UTR (with or without intron, red), or in intron only (blue) g, The impact of Alu on mRNA expression after Ku degradation. The Log2 (mean TPM + 1) in DMSO versus IAA- and Dox-treated (day 4) Ku80-AID samples were plotted. The red and blue dots are genes with annotated Alus in 3′ UTR (with or without Intron, red, n > 2), or in Intron only (blue, n > 9). The data associated with panels f and g can be found in SI Tab. 12 and 13.
