Fig. 6

Differential TSS and TES usage. Pairs of transcript isoforms with significant isoform switches and different TSS (A–D) and TES (E, F). A AT1G11280—the shorter .6 transcript is cold-responsive. B AT3G13110—single-exon gene with different TSS where the .1 transcript has rapid cold-induced expression compared to the .2 transcript. C AT1G55960—both transcripts peak at dusk but have different expression behavior with the .11 isoform showing large increases of expression at 20 °C and day 1 at 4 °C declining with continued cold exposure. D AT5G53420—isoforms with very different TSS - .7 isoform expressed rhythmically peaking during the day (light-responsive) at 20 °C before declining rapidly in the cold while the .12 transcript has increased expression in the cold, peaking during the dark. E AT4G14400—the isoforms differ only in their TES but are expressed rhythmically with different phase (3 h offset) at 20 °C and reduced at 4 °C. F AT3G56860—very different TES and expression behavior—antiphasic at 20 °C with cold-induced switch to the shorter .12 isoform. Error bars on points are standard errors of the mean