Additional file 9 of A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

Additional file 9: Fig. S3. Temperature-regulated alternative polyadenylation. (A-D) 3′ RNA-Seq data obtained from S2R+ cells (A, C) and adult male flies (B, D) after 24 h of incubation at different temperatures (11, 14, 25 and 30 °C) was used for an analysis of temperature effects on the choice of polyadenylation sites (PASs). (A,B) Histograms illustrate the frequency of alternative polyadenylation (APA) in S2R+ cells (A) and adult male flies (B), as detected after pooling all data obtained at the different temperatures from the three biological replicates. In total, 14,669 PASs were detected in S2R+ cells, and 22,378 in adult male flies. These were assigned (see Materials and Methods) to a total of 7495 and 10,757 expressed genes in S2R+ cells and adult male flies, respectively. (C,D) Temperature effects on APA. For genes with multiple PASs, we compared the two PASs with highest presence (read counts) across all conditions and required the log2 fold change to be in opposite directions when comparing the read counts at the high (25 and 30 °C) with those at the low (11 and 14 °C) temperatures. The scatter plots display the fold changes at the proximal and distal of these two most strongly affected PASs in S2R+ cells (C) and adult flies (D). Blue dots represent genes (class I), where preference of the distal over the proximal PAS at low temperature is significant in comparison to the high temperature. Red dots represent genes (class II), where temperature change has a significant effect in opposite direction.