Fig. 3: The position and strength of TDP-43 binding influence polyA site usage.
From: TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes
a, Cumulative plots showing the location of TDP-43 binding relative to TDP-43-regulated polyA sites. b, Volcano plots showing the enrichment of hexamers in different regions surrounding polyA sites. c, Cumulative plots show that TDP-43 KD caused a larger absolute usage change in polyA sites with weak TDP-43 binding (low GU content) than sites with strong TDP-43 binding (high GU content). d, Cumulative plots show that for TDP-43-regulated APA sites, polyA sites with increased usage are stronger than polyA sites with decreased usage. e, Cumulative plots show that for genes with significant 3′ UTR lengthening upon TDP-43 KD, their distal polyA sites are stronger than their proximal ones. PolyA site scores (in d and e) were calculated using Aparent2, expressed as log odds ratio, and reflect polyA site strengths. P values in a and c–e were calculated using two-sided Mann–Whitney U test, and adjusted P values in b were calculated using the Benjamini–Hochberg procedure.