Fig. 5
From: Alternative polyadenylation factors link cell cycle to migration
Changes in polyadenylation site recognition sequences in proximal versus distal polyadenylation sites for genes undergoing APA with quiescence. a Schematic showing the relative position of the UGUA motif, hexamers, the cleavage site and GU/U-rich motifs. b The frequencies with which different possible hexamers are present at the proximal or distal polyadenylation sites are shown for genes that have two polyadenylation sites and shift to the use of more distal polyadenylation sites with quiescence (dark blue). Other hexamers are AAACAU, AAUAAC, UUAAAG, UUAAAU, UAUAAA, AAUACA, CAUAAA, AAUAUA, GAUAAA, AAUGAA, AAGAAA, ACUAAA, AAUAGA, AAUAAU, AACAAA, AUUACA, AUUAUA, AACAAG, and AAUAAG. Data are compared with results for genes that use a proximal polyadenylation site or do not change their use of polyadenylation site with quiescence (light blue). Data are shown for all genes, for genes that undergo UTR APA and for genes that undergo UR APA. Statistically significant differences were determined by Fisher’s exact test (c) The fraction of genes with a UGUA motif in the region upstream of the polyadenylation site hexamer is shown. Data are provided for genes that shift to greater use of distal polyadenylation sites in quiescence (dark blue) and a control set of genes that do not use distal polyadenylaton sites more with quiescence (light blue) (left plots). Data are also provided for genes that shift to greater use of proximal polyadenylation sites with quiescence (brown) and a control set of genes that do not shift to greater use of proximal polyadenylation sites (pink) (right plots) Statistically significant differences were determined by two-tailed Fisher’s exact test. d The fraction of genes with a U-rich motif in the region downstream of the polyadenylation site hexamer are shown. e The fraction of base pairs 20–40 nts downstream from the polyadenylation site that are Us is shown for genes that shift to use of more distal polyadenylation sites with quiescence. Statistical significance was determined by Wilcoxon signed-rank test