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

Normalization with spike-in reads demonstrated highly similar transcription profiles in 528! unconditioned and preconditioned cells ( Figure S1B ; Figure S3C ). This allowed us to utilize 529! also samples generated in our previous study ; GSE71708) that highly 530! correlated (rho=0.96) with the data generated in this study ( Figure S1H ). Since our earlier data 531! did not have spike-in reads we utilized the ends of long genes when normalizing samples 532! between distinct datasets. As described in Mahat et al. (2016) were retained. The level of transcription per each transcript was measured from the gene body 546! (+500 nt from TSS to -500 nt from CPS), as described previously 547! Vihervaara et al., 2017) . In the downstream analyses, we retained a single transcript per gene 548! by selecting the isoform that showed the largest fold change to heat shock, or if called 549! unresponsive to heat stress, had the highest level of transcription in non-stress condition. The 550! . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/576959 doi: bioRxiv preprint ! ! 21! analyses of enriched gene annotation categories were performed with Database for 551! Annotation, Visualization and Integrated Discovery (DAVID; Dennis et al., 2003) . ! 552!