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

The prolonged residence time of Pol II at the CPSs, together with decreased initiation at heat-314! activated genes and enhancers, suggested reduced recycling of the transcription machinery from 315! the ends of active genes to heat-induced transcription. To examine the status of Pol II and 316! processing of transcripts at 5'-and 3'-ends of genes, we analyzed the length distribution of PRO-317! seq reads that overlap either with the transcription start site (TSS) or CPS. In essence, Pol II that 318! undergoes initiation or pausing has transcribed through fewer nucleotides (<60 nt) than the 319! sequenced read length in our PRO-seq data (75 nt). Thereby, the TSS-containing reads report, 320! besides the initiating base (5'-end of the read), also the active site of transcription (3'-end of the 321! read) of each individual transcript ( Figure 6D ; Rasmussen et al. 1993; Nechaev et al., 2010; 322! Tome et al., 2018) . The lower density of promoter-proximal Pol II that was detected after heat 323! shock in preconditioned cells ( Figure 6A ; Figure S5B ), comprised of transcripts with the whole 324! spectrum of PRO-seq read lengths (20 nt to 75 nt), which indicates less initiating, pausing and 325! early elongating Pol II complexes ( Figure 6D ). This reduction in all promoter-proximal Pol II 326! states can be explained by less Pol II molecules engaging into transcription at gene promoters. 327!