A R-loop sensing pathway mediates the relocation of transcribed genes to nuclear pore complexes

Abstract

Nuclear pore complexes (NPCs) have increasingly recognized interactions with the genome, as exemplified in yeast, where they bind transcribed or damaged chromatin. By combining genome-wide approaches with live imaging of model loci, we uncover a correlation between NPC association and the accumulation of R-loops, which are genotoxic structures formed through hybridization of nascent RNAs with their DNA templates. Manipulating hybrid formation demonstrates that R-loop accumulation per se, rather than transcription or R-loop-dependent damages, is the primary trigger for relocation to NPCs. Mechanistically, R-loop-dependent repositioning involves their recognition by the ssDNA-binding protein RPA, and SUMO-dependent interactions with NPC-associated factors. Preventing R-loop-dependent relocation leads to lethality in hybrid-accumulating conditions, while NPC tethering of a model hybrid-prone locus attenuates R-loop-dependent genetic instability. Remarkably, this relocation pathway involves molecular factors similar to those required for the association of stalled replication forks with NPCs, supporting the existence of convergent mechanisms for sensing transcriptional and genotoxic stresses.

Approaches for Mapping and Analysis of R‐loops

“…While studies have shown associations between R-loop formation and changes in chromatin accessibility, histone modifica-tions, and nuclear organization (P. B. Chen et al, 2015;Penzo et al, 2023;Sanz et al, 2016), the causal relationships and mechanistic links remain mostly elusive. Integrative approaches combining chromatin conformation capture techniques with R-loop mapping methods can elucidate how R-loops influence chromatin architecture and gene expression regulation, providing insights into their functional consequences in health and disease.…”

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

“…Li et al, 2023). There is relatively little published work that has directly addressed the question of how selective tethering of RNA to chromatin can be achieved: For S. cerevisiae mutants of the TREX complex, chromatin retention has been convincingly linked to the formation of R-loops (Penzo et al, 2023). In that case, retention coincides with downregulation of the CPAC component Fip1, a co-factor of the poly(A) polymerase, and defects in polyadenylation (Saguez et al, 2008).…”

RNA biogenesis and RNA metabolism factors as R-loop suppressors: a hidden role in genome integrity

“…This process can also induce torsional stress that interferes with fork progression, and indeed, some of the TREX-2 components are targeted by the DNA damage checkpoints to alleviate such an effect ( Bermejo et al 2011 ). However, a recent study proposes that, when formed, R-loops promote the relocation of genes to the nuclear pore in a process that is mediated by RPA and sumoylation to prevent genetic instability ( Penzo et al 2023 ). We still need to define how the nuclear localization (whether in the nucleoplasm or the nuclear periphery) impacts the origin and fate of R-loops.…”