SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots

Uruci, S.; Hoitsma, N. M.; Soler-Oliva, M. E.; Bayona-Feliu, A.; Gaggioli, V.; Rubio, M. L. G.; Lo, C. S. Y.; Bakker, C.; Marinello, J.; Manolika, E. M.; Capranico, G.; Luijsterburg, M. S.; Luger, K.; Aguilera, A.; Taneja, N.

doi:10.1101/2024.09.13.612941

bioRxiv · 10.1101/2024.09.13.612941

SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots

Uruci, S.·Hoitsma, N. M.·Soler-Oliva, M. E.·Bayona-Feliu, A.·Gaggioli, V.·Rubio, M. L. G.·Lo, C. S. Y.·Bakker, C.·Marinello, J.·Manolika, E. M.·Capranico, G.·Luijsterburg, M. S.·Luger, K.·Aguilera, A.·Taneja, N.

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Abstract

DNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series of in vitro and in vivo experiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.

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Uruci, S., Hoitsma, N. M., Soler-Oliva, M. E., Bayona-Feliu, A., Gaggioli, V., Rubio, M. L. G., Lo, C. S. Y., Bakker, C., Marinello, J., Manolika, E. M., Capranico, G., Luijsterburg, M. S., Luger, K., Aguilera, A., Taneja, N.. 2024-09-15. SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots. https://doi.org/10.1101/2024.09.13.612941

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