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New insights into how B cells time the duplication of their genome

11 Dec 2023
AI-generated illustration of the study (generated with midjourney)

In humans, two meters of DNA must be replicated and evenly shared between newly divided cells during every cell cycle. While some regions are duplicated early, others must wait their turn. In a study now published in Nature Communications, scientists in the lab of Rushad Pavri investigate the protein RIF1 and its unique role in regulating the timing of DNA replication in B cells.

During the cell cycle, the entire genome must be duplicated, with one copy being allocated to each daughter cell. The timing of this phenomenon is critical, as it influences the genome’s integrity and function.

In mammals, different regions of the genome are replicated with different timing. Regions that replicate early are generally actively transcribed and thus vital for the cells identity; regions that replicate late are silent and have been shown to accumulate more replication-associated mutations. Replicating early provides more time to repair damaged DNA (especially in transcribed regions) prior to cell division and hence cells use this mechanism to protect the integrity of active genes. Disruptions in replication timing are implicated in various genetic diseases, including cancer.

In a study published in 2022, Rushad Pavri and his lab showed that minichromosome maintenance complex (MCM) proteins were crucial to maintain correct replication timing. In a follow-up investigation, they focused on the protein RIF1 as another important regulator of replication timing and studied its role in B cell genomes and the interplay with the MCM complex. Their findings are now published in Nature Communications.

RIF1’s double identity

RIF1 is a multifunctional protein traditionally known for its role in regulating late replication of silent regions: in most cells, once RIF1 is removed, regions that normally replicate late do so too early, thereby jeopardising cellular health. However, the research team uncovered an unexpected facet of RIF1 in B cells. Contrary to its established function, RIF1 acts as a modulator of early replication in B cells, working in collaboration with MCM proteins.

“The role of RIF1 in B cells was a surprise for us in light of previous findings from other cell types,” says Mihaela Peycheva, co-first author. “To solve that puzzle, we reached out to experts on RIF1 and replication timing who provided us with important supporting data which confirmed our results and led to a fruitful collaboration.”

“We found that B cells need both RIF1 and MCM proteins to maintain a normal replication timing program: if we deplete both, early replicating regions start replicating late. As far as we know, these results only apply to B cells,” says Daniel Malzl, co-first author and master’s student at the time.

Four people in two rows, two sitting on a couch and two standing behind them, smiling at the camera. Behind them is a massive bookshelf.
Left to right, top to bottom: Tobias Neumann, Rushad Pavri, Daniel Malzl, Mihaela Peycheva

Strict timing might prevent unwanted mutations

B cells are unique in that they naturally mutate and rearrange their antibody genes to generate a vast diversity of antibodies, but this process can cause other genomic regions to mutate as well. “This dynamic environment provides a possible explanation why B cells have repurposed RIF1 to promote early replication along with MCM proteins. In essence, we think that RIF1 acts as an additional mechanism to protect active genes in mutating and rapidly dividing B cells, so that B cells have sufficient time to repair damaged DNA before they divide,” speculates Tobias Neumann, co-corresponding author supervising the computational part of the study.

The findings provide crucial insights into the regulation of DNA replication timing in B cells, shedding light on the previously unknown role of RIF1 in promoting early replication.

“This study was a real team effort, both within my lab where bioinformaticians and biologists combined their expertise to lead this project, but also with international experts in the field who provided valuable data and conceptual inputs,” says Rushad Pavri.

Original publication

Daniel Malzl*, Mihaela Peycheva*, Ali Rahjouei, Stefano Gnan, Kyle N. Klein, Mariia Nazarova, Ursula E. Schoeberl, David M. Gilbert, Sara C. B. Buonomo, Michela Di Virgilio, Tobias Neumann# and Rushad Pavri#: “RIF1 regulates early replication timing in murine B cells”. Nature Communications (2023). DOI: 10.1038/s41467-023-43778-y.
* co-first authors
# co-corresponding authors

Further reading

Outgoing talent: Rushad Pavri

Scientists uncover secret behind lymphoma-associated mutations

How distant DNA segments come together to make different types of antibodies