Replication Fork Dynamics in Genome Stability

DNA replication proceeds through specialised structures known as replication forks, where parental duplex DNA is unwound and copied. The faithful progression and stability of these forks are essential for preserving genome integrity. When forks encounter obstacles such as DNA lesions, secondary structures or protein–DNA complexes, they can stall, reverse or collapse, giving rise to single-stranded DNA gaps and other intermediates that threaten chromosome stability. Cells deploy a network of enzymatic activities—including nucleases, helicases, polymerases and recombination factors—to process and restart stalled forks, thereby preventing the accumulation of DNA breaks and mutations. Faulty regulation of fork dynamics underlies diverse pathologies, from congenital genome-instability syndromes to cancer chemoresistance. Recent work has illuminated how bidirectional nucleolytic trimming converts nascent gaps into double-strand breaks, how modification of replication factors influences gap formation and fork protection, and how the interplay between replisome components and DNA repair pathways modulates cellular responses to genotoxic stress. These insights point to novel biomarkers and intervention points for genome-directed therapies.

Research from Nature Portfolio

Recent studies have revealed that replication stress-induced single-stranded DNA gaps are actively processed by nucleases in a stepwise manner. In one investigation, MRE11 and EXO1 were shown to expand and convert gaps into double-strand breaks, a process suppressed by homologous-recombination factors under normal conditions. Another report demonstrated that inhibition of PARP1 impairs maturation of Okazaki fragments and increases post-replicative single-strand nicks, highlighting unligated nascent fragments as a source of genomic instability when PARP activity is compromised. Complementary findings indicate that PCNA ubiquitination not only directs lesion bypass but also stabilises forks under unperturbed growth by preventing DNA2-mediated degradation; loss of this modification leads to defective gap-filling, nascent strand resection and sensitisation to fork-targeting agents. Together, these works chart how nuclease activities and post-translational modifications of replication factors coordinate fork protection and gap resolution to safeguard genome stability.

Research from all publishers

Investigations outside the portfolio have characterised regulators of repriming and resection at stalled forks. One study identified the deubiquitinase USP1 as a key promoter of PRIMPOL-dependent repriming gaps and their expansion by MRE11 and EXO1, linking PCNA deubiquitination to increased gap accumulation during replication stress. Work on prelamin A-expressing cells revealed that aberrant lamin processing elevates baseline replication stress by enhancing MRE11-mediated resection and downregulating Fanconi anaemia pathway components, thereby exacerbating genomic instability and senescence. In a tumour context, overexpression of the mismatch-repair protein MLH1 was found to interact with FEN1 to restrain DNA2 activity on regressed forks of BRCA2-deficient cells, reducing R-loop formation and stabilising replication intermediates to support cell viability. These studies emphasise how modulation of repriming, resection and protein–protein interactions determines fork fate in diverse genetic backgrounds.

Replication Fork Dynamics in Genome Stability publication trend

The graph below shows the total number of articles in replication fork dynamics in genome stability across all publications each year (not limited to Nature Index journals).

Technical terms

Replication fork: The Y-shaped structure formed when DNA helicase unwinds duplex DNA during replication.

ssDNA gap: A stretch of single-stranded DNA arising when synthesis is skipped or stalled, often requiring processing or repair.

Fork reversal: The conversion of a stalled fork into a four-way junction by annealing of nascent strands, which can protect or expose DNA ends.

Nuclease: An enzyme that cleaves DNA strands, sometimes leading to controlled trimming or pathological degradation of forks.

PCNA ubiquitination: The attachment of ubiquitin to the sliding clamp PCNA, modulating lesion bypass, fork stability and Okazaki fragment maturation.

Homologous recombination: A high-fidelity repair pathway that restores broken forks using a homologous template, often mediated by RAD51 and BRCA proteins.

References

1. Multi-step processing of replication stress-derived nascent strand DNA gaps by MRE11 and EXO1 nucleases. Nature Communications (2023).
2. PARP inhibition impedes the maturation of nascent DNA strands during DNA replication. Nature Structural & Molecular Biology (2022).
3. Ubiquitinated-PCNA protects replication forks from DNA2-mediated degradation by regulating Okazaki fragment maturation and chromatin assembly. Nature Communications (2020).
4. USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress. Nucleic Acids Research (2024).
5. The Compromised Fanconi Anemia Pathway in Prelamin A‐Expressing Cells Contributes to Replication Stress‐Induced Genomic Instability. Advanced Science (2024).
6. Mismatch repair protein MLH1 suppresses replicative stress in BRCA2 deficient breast tumors. Journal of Clinical Investigation (2024).