Head-on collisions between the replication and transcription machinery over R-loopforming sequences potently stall replication forks. Stalled fork structures can then be converted into DNA breaks, leading to apoptosis or growth arrest of cycling cells. The mechanisms which coordinate transcription and replication to avoid these genotoxic collisions are therefore critical for cellular fitness, especially in the case of rapidly dividing tumor cells. However it is unclear if coordination occurs passively through globally encoded co-directionality between transcription units and replication forks, or actively, through transcriptional regulatory mechanisms that function to silence head-on transcripts during S-phase. ‘Active’ coordination would imply that transcriptional regulators could be effectively targeted in cancer to induce collisions and subsequent tumor cell killing. However, the ‘active’ coordination model has never been systematically assessed. In this dissertation, we present work demonstrating that head-on transcription over R-loop forming sequences occurs at a high frequency during the cell cycle across tumor cell types, that this transcription is temporally downregulated during S-phase, and that INO80 and MOT1 are leveraged in NSCLC to suppress genotoxic TRCs and preserve tumor cell viability. These results suggest that transcriptional regulation is imperative to genome stability, and transcriptional regulators serve as promising targets for the treatment of NSCLC.