image: The MCM helicase is broadly bound across the genome, and its phosphorylation is antagonistically regulated by the kinase DDK and the phosphatase RIF1–PP1. TRESLIN–MTBP recognises the phosphorylated MCM helicase, thereby determining where DNA replication initiates (left). Activation of the MCM helicase then leads to the formation of replication forks (right).
Credit: © The Kanemaki laboratory at National Institute of Genetics
When cells proliferate, genomic DNA is precisely duplicated once per cell cycle. Abnormalities in this DNA replication process can cause alterations in genomic DNA, promoting cellular ageing, cancer, and genetic disorders. Therefore, understanding how cells replicate their DNA is crucial for elucidating fundamental biological processes, diseases, and even evolution.
Traditionally, DNA replication has been studied in microorganisms such as E. coli and yeast. In these organisms, the location where DNA replication begins (replication origin) is determined by a specific DNA sequence. However, in most eukaryotic cells, including human cells, the DNA sequence itself does not dictate where replication starts. For decades, it remained a mystery how and where replication is initiated within the human genome.
To address this, Professor Masato Kanemaki and his team at National Institute of Genetics developed a new high-precision method, LD-OK-seq (Ligase Depletion-Okazaki sequencing), to detect replication initiation sites in the human genome. By further analysing the proteins bound to these regions, they uncovered the fundamental principle by which human cells determine replication initiation sites.
Their findings revealed that, except for actively transcribed gene regions, human cells possess the ability to initiate DNA replication from almost anywhere in the genome. This capability arises from the widespread binding of an enzyme called the MCM helicase, which is essential for DNA replication. Moreover, they discovered that during the early S phase, replication frequently begins in intergenic regions (areas between transcribed genes), and that these sites are determined by the binding of TRESLIN-MTBP, a protein complex that activates the MCM helicase. They also identified an antagonistic regulatory system that modulates the binding of TRESLIN-MTBP to the MCM helicase.
These discoveries answer the fundamental question of how human cells initiate genome replication, providing new insights into diseases caused by replication abnormalities—such as genomic instability disorders, cancer, aging, and genetic disorders—as well as into genome evolution. In the long term, this work may also lay the foundation for technologies that enable artificial control of DNA replication.
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About National Institute of Genetics (NIG)
National Institute of Genetics (NIG) was established to carry out broad and comprehensive research in genetics. NIG contributes to the development of academic research as one of the inter-university research institutes constituting the Research Organization of Information and Systems (ROIS).
About the Research Organization of Information and Systems (ROIS)
ROIS is a parent organization of four national institutes (National Institute of Polar Research, National Institute of Informatics, the Institute of Statistical Mathematics and National Institute of Genetics) and the Joint Support-Center for Data Science Research. It is ROIS's mission to promote integrated, cutting-edge research that goes beyond the barriers of these institutions, in addition to facilitating their research activities, as members of inter-university research institutes.
Journal
Nature Communications
Article Publication Date
2-Dec-2025