Figure 2

Extensive 3' UTR shortening in proliferative cells. (a) Two examples of transcripts that showed enhanced usage of proximal CSs in BJ proliferating cells compared to confluent ones. The blue and red plots correspond to genes encoded on the positive and reverse strands, respectively. Proximal and distal CSs are indicated by green and orange triangles, respectively. Ratios between proximal and distal peak levels are indicated to the right. (b) The proximal polyadenylation site usage index (proximal PUI) provides a global measure for the relative usage of proximal CSs in the examined conditions (Materials and methods). The transition from proliferation to confluent state resulted in a strong decrease in the proximal PUI. (c) A pie chart showing the distribution of transcripts that underwent significant change in CS usage in the transition from proliferation to confluent. In dark and light blue are the proportions of transcripts with shortened or lengthened 3' UTRs in the proliferative state, respectively. (d) The proliferative status of proliferating and confluent BJ cells was measured using a proliferation index, which is based on the relative expression of cell-cycle related genes. (e-g) Same as (b-d), but here proliferating and serum-deprived MCF10A cells were analyzed.