The 7SK small nuclear ribonucleoprotein links the cell responses to transcription and replication stress by promoting replication fork reversal and homologous recombination

Bowry, A.; Wilson, C.; Kelly, R. D. W.; Wilkins, R. J.; Walker, A. K.; Varghese, C. S.; Murphy-Hollies, S.; Morris, J. R.; Kanhere, A.; Petermann, E.

doi:10.1101/2025.09.30.678750

bioRxiv · 10.1101/2025.09.30.678750

The 7SK small nuclear ribonucleoprotein links the cell responses to transcription and replication stress by promoting replication fork reversal and homologous recombination

Bowry, A.·Wilson, C.·Kelly, R. D. W.·Wilkins, R. J.·Walker, A. K.·Varghese, C. S.·Murphy-Hollies, S.·Morris, J. R.·Kanhere, A.·Petermann, E.

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Abstract

The 7SK-small nuclear ribonucleoprotein complex (7SK-snRNP) plays a crucial role in the response to transcription stress, releasing positive transcription elongation factor P-TEFb to sustain RNA polymerase II activity when transcription is blocked. Many conditions that block transcription also block DNA replication, causing replication stress, and 7SK-snRNP components are putative tumour suppressors with roles in transcription-replication conflicts and double-strand break repair. Here, we investigate potential roles of 7SK-snRNP components in the response to replication stress induced by chemotherapy agents with and without additional impact on transcription. We report that HEXIM1 and LARP7 promote replication fork slowing in response to agents that cause both replication- and transcription stress, in a manner consistent with their canonical 7SK-snRNP functions. Our data suggest that this role in fork slowing is mainly through facilitating RAD51-mediated replication fork reversal rather than transcription-replication conflicts. HEXIM1 and LARP7 promote RAD51 recruitment to replication-associated DSBs or post-replicative gaps under conditions of transcription stress such as induced by camptothecin or BET inhibitors and support HR at direct DSBs. In contrast, HEXIM1 and LARP7 are not required for HR in response to hydroxyurea, which does not cause transcription stress. Our data support that LARP7 roles during replication stress are independent of its reported interaction with BRCA1, and that both LARP7 and HEXIM1 promote survival in response to replication stress-inducing agents. 7SK-snRNP components are not recruited to stressed replication forks and RNA polymerase II inhibition phenocopies loss of these proteins. Taken together, our data support a model where 7SK-snRNP modulation of RNA polymerase II activity helps facilitate RAD51 function under transcription stress conditions, thereby connecting the cell responses to transcription- and replication stress.

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Bowry, A., Wilson, C., Kelly, R. D. W., Wilkins, R. J., Walker, A. K., Varghese, C. S., Murphy-Hollies, S., Morris, J. R., Kanhere, A., Petermann, E.. 2025-09-30. The 7SK small nuclear ribonucleoprotein links the cell responses to transcription and replication stress by promoting replication fork reversal and homologous recombination. https://doi.org/10.1101/2025.09.30.678750

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