DNA Replication, Transcription and R-loops (Stephan Hamperl)

In this episode of the Epigenetics Podcast, we talked with Dr. Stephan Hamperl from the Helmholtz Zentrum Munich about his work on how conflicts between transcription, replication, and R-loop formation influence genome stability in human cells.

During the early stages of his career Stephan studied conflicts between transcription and replication in human cells, particularly focusing on R-loop structures. In our discussion, he explains the formation of R-loops and their impact on genome stability, emphasizing the importance of the orientation of replication forks approaching R-loops in determining DNA damage outcomes.

Stephan then delves into his work on the MATAC-Seq method, which analyzes chromatin domains at DNA replication origins to understand replication timing variability. The method involves methylating DNA linkers between nucleosomes and using nanopore sequencing for single-molecule readouts, revealing heterogeneity in chromatin structure at replication origins.

Finally, Stephan discusses his automated image analysis pipeline for quantifying transcription and replication activity overlap in mammalian genomes, addressing the challenge of visualizing these processes simultaneously. The conversation concludes with insights into Stefan's future research directions, focusing on understanding transcription-replication conflicts' molecular basis and their potential implications in cancer cell transformation.

References

• Hamperl, S., Brown, C. R., Garea, A. V., Perez-Fernandez, J., Bruckmann, A., Huber, K., Wittner, M., Babl, V., Stoeckl, U., Deutzmann, R., Boeger, H., Tschochner, H., Milkereit, P., & Griesenbeck, J. (2014). Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic acids research, 42(1), e2. https://doi.org/10.1093/nar/gkt891

• Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T., & Cimprich, K. A. (2017). Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell, 170(4), 774–786.e19. https://doi.org/10.1016/j.cell.2017.07.043

• Chanou, A., Weiβ, M., Holler, K., Sajid, A., Straub, T., Krietsch, J., Sanchi, A., Ummethum, H., Lee, C. S. K., Kruse, E., Trauner, M., Werner, M., Lalonde, M., Lopes, M., Scialdone, A., & Hamperl, S. (2023). Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic acids research, 51(22), 12303–12324. https://doi.org/10.1093/nar/gkad1022

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