Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids

AUTHORS

Stoy HHenriette , Zwicky KKatharina , Kuster DDanina , Lang KSKevin S , Krietsch JJana , Crossley MPMagdalena P , Schmid JAJonas A , Cimprich KAKarlene A , Merrikh HHoura , Lopes MMassimo . Nature structural & molecular biology. 2023 3 2; 30(3). 348-359

PMID: 36864174[PubMed].

ABSTRACT

Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.

Tags: 2023