Fig. 2

Alternative polyadenylation is associated with RNA localization in a variety of cell types. (A) Comparison of ψ values for RNA isolated from cell projections and cell bodies. ψ values for all genes were calculated using RNA collected from cell projection and cell body compartments, and genes with significantly different ψ values across compartments were identified (FDR < 0.05). Δψ values (cell projection - cell body) for these genes are indicated by boxplots. P values in blue represent binomial p values for deviations from the expected 50% chance for a gene to have a positive Δψ value. Samples were also separated according to the amount of time that projections were allowed to grow before their RNA content was analyzed. This is represented by the long (at least 6 days) and short (2 days or less) categories colored in red. (B) As in A, ψ values for all genes were calculated using RNA collected from cell projection and cell body compartments, and genes with significantly different ψ values across compartments were identified (FDR < 0.05). The fraction of significant tandem UTR and ALE genes with positive Δψ values were plotted on the x and y axes, respectively. (C) Simplex plot indicating ψ values calculated from RNA isolated from biochemically defined cytosolic, membrane-associated, and insoluble fractions of HepG2 cells. Genes with equal ψ values in all three fractions are represented by dots equidistant from each vertex (at the intersection of the dotted lines). Genes that displayed higher ψ values in a given fraction than the others are represented by dots placed closer to that fraction’s vertex. Red lines indicate the density of dots. (D) Comparison of ψ values in HepG2 cytosolic and membrane fractions for genes whose ψ value was significantly different between these compartments (FDR < 0.01). (E) Correlation of Δψ values (membrane - cytosol) for all genes expressed in both HepG2 and K562 cells. (F) Fraction of genes with nonsignificant Δψ values (membrane vs. cytosol, gray) and those with significant Δψ values (red) that encode peptides that have ER signal sequences as defined by SignalP. Distributions of this fraction were created through bootstrapping in which 40% of the genes were sampled 100 times. P values were calculated using a Wilcoxon rank sum test