Elongation factor ELOF1 drives transcription-coupled repairand prevents genome instability [DRB-TTchem-seq]

Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA Polymerase II (Pol II), causing transcription inhibition and transcription-replication conflicts. Cells have evolved intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions, however the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR/cas9 screen, we identified elongation factor ELOF1 as an important new factor in the damage-induced transcription stress response. ELOF1 has an evolutionary-conserved role in TC-NER where it promotes the recruitment of the TC-NER factors UVSSA and TFIIH and facilitates Pol II ubiquitylation to efficiently repair TBLs. Importantly, ELOF1 has an additional role in protecting cells from transcription-mediated replication hindrance, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage by two distinct mechanisms. Overall design: Determining the elongation rates in HCT116 wt, ELOF1 KO, CSB KO or ELOF1 KO+ ELOF1-GFP cells using DRB-TTchem-seq. transient transcriptome sequencing (TT-seq); 3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-ß-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)