The Molecular Basis of Transcription-Replication Conflicts and Pathways to Resolution

/Abstract: Transcription and replication machineries frequently collide, leading to transcription-replication conflicts that destabilize the genome if not resolved, which contributes to diseases such as cancer. Despite their destructive potential, the mechanisms behind these conflicts and their resolution are poorly understood. This proposal aims to identify novel factors involved in resolving these conflicts, define how they form, and provide mechanistic insights into their resolution. By combining computational predictions, advanced biochemistry, and cryo-EM, this research will reveal how genomic stability is maintained in the face of these conflicts. During the beginning of my postdoc, I investigated how genome stability is maintained through the recruitment of key factors, demonstrating that the transcription machinery directly promotes the deposition of a histone modification that recruits stability-maintaining factors. I am now focused on understanding transcription-replication conflicts, a critical source of genome instability. I have already purified the necessary components for this project and visualized interactions between transcription machinery and stability-promoting factors, as well as replication machinery with a genome-stabilizing factor. In Aim 1, I will use AlphaFold predictions to identify novel factors recruited to transcription-replication conflicts and employ cryo-EM to visualize their interactions with the transcription or replication machinery. Aim 2 will reconstitute transcription-replication conflicts in vitro, enabling manipulation and visualization of these reactions to understand how various factors contribute. In Aim 3, I will investigate how the Integrator Complex works with replication machinery to resolve conflicts. During the K99 phase, I will develop systems for reconstituting and manipulating transcription- replication conflicts under expert mentorship. This training will provide the skills necessary for independent research in the R00 phase, where I will define the molecular mechanisms of conflict resolution. My research aligns with the NIH’s mission to advance biomedical knowledge and improve human health. By uncovering mechanisms behind transcription-replication conflicts, my work will enhance our understanding of genome stability and contribute to preventing diseases such as cancer. My environment offers cutting-edge technology, expert mentorship, and a collaborative community, positioning me to make meaningful contributions to the field and establish myself as a successful, independent researcher. Project Number: 1K99GM163010-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Jonathan markert | Institution: HARVARD MEDICAL SCHOOL, BOSTON, MA | Award Amount: $125,000 | Activity Code: K99 | Study Section: Special Emphasis Panel[ZRG1 CDB-Z (80)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11281797