CFAP20 accelerates RNAPII elongation from promoters to prevent conflicts with co-directional replisomes

Fine-tuning the coexistence of DNA replication and transcription is essential to avoid detrimental collisions between these two machineries. This is particularly relevant at promoters, as RNA polymerase II (RNAPII) elongation is slowest there, and DNA replication evolutionarily initiates in close proximity to these sites. The mechanisms that regulate the acceleration of RNAPII to specifically avoid conflicts with the incoming replisome in a co-directional manner have not been addressed. In this study, using genome-wide and proteomics approaches, we identify and characterize CFAP20 as part of a protective pathway that accelerates elongating RNAPII, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops specifically at promoters and display defects in origin firing and replication fork progression. Co-depletion of the Mediator complex, or removal of RNAPII engaged with R-loops, completely rescues these replication phenotypes. Therefore, we propose that CFAP20 aids in RNAPII acceleration under conditions of high Mediator-driven transcription output to fine-tune RNAPII elongation and prevent collisions with co-directional replisomes.