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Basille, A.* ; Bawadi, Y.* ; Lin, Y.* ; Kirke, C.* ; Bourgeay, C.* ; Cluet, D.* ; Vachez, L.* ; Dervieux, V.* ; Guiguettaz, L.* ; Bernard, P.* ; Hamperl, S. ; Pasero, P.* ; Ricci, E.P.* ; Vanoosthuyse, V.*

The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids.

EMBO J., DOI: 10.1038/s44318-026-00949-z (2026)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Multiple lines of evidence suggest that RNase H1-sensitive RNA:DNA hybrids could disrupt the stability and restart of stalled replication forks. The prolonged over-expression of RNase H1 is the most popular method to manipulate RNA:DNA hybrids in situ but it cannot discriminate between direct and indirect effects resulting from their loss. To overcome this limitation, we developed iCoRD (in Cellulo RNase H Delivery) to rapidly deliver comparable amounts of either Escherichia coli RNase H1 (RnhA) or control proteins in live cells, with a negligible impact on the transcriptome. iCoRD-delivered RnhA recognises RNA:DNA hybrids in situ, is enriched in the vicinity of active replication forks and rescues replication fork progression in different stress conditions. While iCoRD-delivered RnhA had a clear impact on stress-induced, fork-proximal RNA:DNA hybrids and R-ChIP signals, it had no effect on DRIP or S9.6 Cut&Tag signals, even when these were induced by stress. Our results strongly suggest the existence of distinct populations of RNA:DNA hybrids that are best mapped by different methods and are differently sensitive to RNase H1 activity in situ.
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Publication type Article: Journal article
Document type Scientific Article
ISSN (print) / ISBN 0261-4189
e-ISSN 1460-2075
Journal EMBO Journal, The
Publisher Springer
Publishing Place Heidelberg, Germany
Reviewing status Peer reviewed
Institute(s) Institute of Epigenetics and Stem Cells (IES)
Grants IDEXLYON
Fondation ARC pour la Recherche sur le Cancer (ARC)
EC | Horizon Europe | Excellent Science | HORIZON EUROPE European Research Council (ERC)
Laboratoire d'Excellence Ecofect (LabEx Ecofect)
Fondation pour la Recherche Medicale (FRM)
Ligue Contre le Cancer (laliguecancer)
Agence nationale de la recherche (ANR)