Stress-Induced Transcriptional Memory Accelerates Promoter-Proximal Pause-Release and Decelerates Termination over Mitotic Divisions

Anniina Vihervaara; Dig Bijay Mahat; Samu V. Himanen; Malin A.H. Blom; John T. Lis; Lea Sistonen

Since individual genes and whole transcription programs can be coordinated at the promoter-128! proximal pause-release (Rougvie and Lis, 1988; Boettiger and Levine, 2009; Mahat et al., 2016; 129! Vihervaara et al., 2017) , we addressed whether the changed pausing pattern in daughter cells 130! alters genes' heat responsiveness. We preconditioned MEFs with a single 1-hour heat shock, and 131! allowed a 48-hour recovery before measuring transcription kinetics provoked by an additional 132! heat shock. To capture instant and sustained changes in heat-induced transcription, we conducted 133! ! ! 7! heat-induced genes, such as Ubc that encodes polyubiquitin ( Figure 2B ), gained promoter-136! proximal Pol II pausing during preconditioning (0-minute inset in Figure 2B ), and released the 137! paused Pol II faster into elongation upon heat shock (12.5-minute inset in Figure 2B ). By 40 138! minutes of heat shock, unconditioned cells also had gained high Ubc transcription and efficient 139! Pol II pause-release ( Figure 2B ), suggesting that preconditioning accelerated the onset, rather 140! than changed the overall level of transcription. The faster activation was also demonstrated by 141! heat-induced waves of Pol II progression: For example at Vinculin (Vcl) gene, the advancing 142! wave of transcription had proceeded farther during the 12.5-minute heat shock in preconditioned 143! than in unconditioned cells ( Figure 2C ). This transiently activated gene had returned to its basal 144! expression by 40 minutes of heat shock, regardless of the preconditioning ( Figure 2C ). 145! Importantly, Vcl did not show higher pausing in preconditioned cells (0-minute inset of Figure 146 ! 2C), but the altered usage of promoter-proximal pause sites and the lower pausing signal upon 147! heat stress (insets of Figure 2C ) indicated faster kinetics of Pol II when proceeding from its 148! promoter-proximal pause to productive elongation.! 149!