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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response
Sophie C van der Horst1, Leonie Kollenstart1,2, Amandine Batté1
1Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Nature Communications
|February 6, 2025
Summary
Researchers identified 423 genes regulating DNA replication using a new method called Replication-IDentifier (Repli-ID). This tool tracks DNA polymerase epsilon (Pol ε) in yeast mutants, revealing key proteins like LGE1 and ROX1 involved in replication stress response.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- DNA replication is crucial for cell division, and its perturbation can lead to replication fork stalling or collapse.
- A complex replication stress response network exists to stabilize forks and activate checkpoints, but many involved proteins remain unknown.
Purpose of the Study:
- To develop a genome-wide method for identifying regulators of DNA replication.
- To uncover novel proteins and pathways involved in the cellular response to replication stress.
Main Methods:
- Development of Replication-IDentifier (Repli-ID), a technique combining chromatin immunoprecipitation (ChIP) with next-generation sequencing.
- Tracking replicative polymerase epsilon (Pol ε) at barcoded origins of replication in thousands of hydroxyurea-treated yeast mutants.
Main Results:
- Identification of 423 genes that promote Pol ε binding at replication forks, including LGE1 and ROX1.
- Mechanistic insights: Lge1 influences replication initiation/stability via H2B mono-ubiquitylation; Rox1 impacts fork progression, S-phase entry, and checkpoint activation through ceramide levels.
Conclusions:
- Repli-ID is a powerful resource for discovering DNA replication regulators.
- The study elucidates novel roles for LGE1 and ROX1 in maintaining genome stability under replication stress.
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