Fig. 3

Acute induction of APC loss in colon organoids drives global dysregulation of poly(A) site selection. A Scatter plot of the difference in gene level 3′ UTR lengths in human colon organoids with APC gene knockout using CRISPR/Cas9 comparing 0- versus 24-h timepoints. 3′ UTRs that show significant shortening are indicated in green lengthening are indicated in purple. B Fraction of 3′ UTRs identified in colon organoids as lengthened, shortened, or no change (panel A) that contain at least one of the five most significantly enriched motifs (CSGGCCMC, GCCCCS, GGGGGAS, CGGSCC, CCCWGSCC) identified from colorectal adenocarcinoma de novo motif enrichment analysis (Fig. 2D). P values were calculated using a Chi-squared test compared to the 3′ UTRs in the no change group; error bars reflect 95% confidence interval using bootstrapping. C, E, G Bam coverage plots of RNA-seq data for individual 3′ UTRs (NMT1, CALML4, ALG13) that display lengthening 24 h after APC knock out. Plots are overlaid for time 0 (gray, n = 3) or 24 h (yellow, n = 3). D, F, H Boxplots of 3′ UTR length quantified per gene using APAlyzer, values reflect log₂(distal/proximal reads). P value reflective of a two-sided Student’s T-test