AI-Driven Insights into Replication Fork Stalling: Molecular Mechanisms and Their Impact on Human Genome Stability – RepliVar-AI

The duplication of genetic material is governed by DNA replication, where the replisome duplicates both strands of DNA. However, the replisome often encounters obstacles leading to replication stress, which results in Replication Fork Stalling (RFS). Though some repetitive regions as ribosomal DNA are known to be prone to RFS, the full extent of RFS regions in the human genome remains poorly understood. RFS increases the likelihood of DNA damage, such as double-strand breaks, which can lead to the formation of Structural Variants (SVs) through homologous recombination or replication-based mechanisms.
Our central hypothesis is that RFS regions serve as preferential sites for SV formation. This idea is supported by literature and our preliminary data linking RFS regions with specific molecular signatures and SV formation. The project is structured around two key objectives: (1) identifying molecular signatures that predict RFS regions under different experimental conditions, and (2) determining whether these signatures are associated with SV formation.
for these objectives, four work packages are proposed:
WP1 will focus on experimental mapping of RFS regions during normal and stress-induced S-phase, including drug treatments and protein inactivation experiments.
WP2 aims to identify the molecular signatures of RFS using AI and machine learning, exploiting genomic databases to discover complex patterns associated with RFS regions, and 'exporting' this knowledge to other metazoan genomes.
WP3 will involve creating a synthetic RFS model in human cell lines, allowing us to study the establishment and resolution of RFS in a controlled environment.
WP4 will assess the role of RFS in genetic instability by mapping and analysing the formation of Svs to understand the impact of RFS on genome integrity. Bioinformatics work will also aim to demonstrate the same correlations between RFS and Svs in other metazoan genomes.
The project will combine experimental and computational approaches to define the role of RFS in SVs formation and genomic instability in human cells, but also to explore these hypotheses in other genomes to gain a new perspective on evolutionary aspects.