Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation

Madison Caballero, Tiffany Ge, Ana Rita Rebelo, Seungmae Seo, Sean Kim, Kayla Brooks, Michael Zuccaro, Radhakrishnan Kanagaraj, Dan Vershkov, Dongsung Kim, Agata Smogorzewska, Marcus Smolka, Nissim Benvenisty, Stephen C. West, Dieter Egli, Emily M. Mace, Amnon Koren*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Cellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-Acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. Cells from a single patient carrying MCM10 mutations demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in the mutated MCM10 cells were predominantly comprised of replication delays and initiation site gains and losses. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel candidate modulator of DNA replication timing.

Original languageAmerican English
Pages (from-to)2899-2917
Number of pages19
JournalHuman Molecular Genetics
Issue number17
StatePublished - 1 Sep 2022

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