Figure 4. Differential miRNA-mediated repression is often due to alternative 3'UTR isoform usage.

(A) Genes with differential AIRs are enriched in genes that are differentially repressed. As in Figure 1D, but highlighting genes with significantly different repression that also have wContext+ score differences ≥ 0.03 (orange).

(B) Higher AIR of CHURC1 miR-155 sites in HeLa compared to HEK293 cells. Otherwise, as in Figure 2A.

(C) Greater miR-155 repression of CHURC1 in HeLa cells. Plotted are the wContext+ and expression change for CHURC1 in HeLa (pink) and HEK293 (blue) cells.

(D, E) As in (B, C), except for ATAD2B, a gene with higher AIR and greater miR-155 repression in HEK293 cells.

(F) As in (A), except comparing changes mediated by miR-124 in HeLa and HEK293 cells.

(G) As in (C), except for ANTXR2, a gene with higher AIR and greater miR-124 repression in HeLa cells.

(H) As in (A), except comparing changes mediated by miR-124 in HEK293 and HeLa cells.

(I) As in (C), except for CLDN1, a gene with higher AIR and greater miR-124 repression in HeLa cells

(J) Direct measurements of miR-155-mediated repression of 3'UTR segments from nine genes initially classified as differentially regulated despite having similar AIRs. Renilla luciferase reporters followed by 3'UTR segments (with either wild-type or mutated miR-155 sites) from the indicated genes were transfected into either HeLa or HEK293 cells in the presence of the cognate (miR-155) or a non-cognate (miR-1) miRNA. Five genes were repressed more in HeLa cells in the genome-wide analyses (highlighted in pink), and four were repressed more in HEK293 cells (highlighted in blue). Plotted are the normalized repression values, with error bars representing the third largest and third smallest values. Significance was calculated with the Mann-Whitney U-test (*, P < 0.05, **, P < 0.01, *** P < 0.001).