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DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

ABSTRACT: Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. Further suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ?, liberating the TOP1i-induced topoR-loop accumulation and genome instability in atm. Additionally, we find a highly conserved junction domain between the exonuclease and polymerase domains in POL2A that is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication is in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a presumably conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE216170 | GEO | 2023/11/03

REPOSITORIES: GEO

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A cell cycle switch in TRF2 controls t-loop dynamics and DNA secondary structure resolution across the genome

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2019-11-25 | PXD014843 | Pride

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Project description:Non-scheduled R loops represent a major source of DNA damage and replication stress. Cells have different ways to prevent R loop accumulation. One mechanism relies on the conserved THO complex in association with co-transcriptional RNA processing factors including the RNA-dependent ATPase UAP56/DDX39B and histone modifiers such as the SIN3 deacetylase in humans. We investigated the function of UAP56/DDX39B in R loop removal. We show that UAP56 depletion causes R loop accumulation, R loop-mediated genome instability and replication fork stalling. We demonstrate an RNA-DNA helicase activity in UAP56 and that its overexpression suppresses R loops and genome instability induced by depleting 5 different unrelated factors. UAP56/DDX39B localizes to active chromatin and prevents the accumulation of RNA-DNA hybrids over the entire genome. We propose that, in addition to its RNA processing role, UAP56/DDX39B is a key helicase required to eliminate harmful co-transcriptional RNA structures that otherwise would block transcription and replication.

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