An evolutionarily conserved protein keeps chromosomes from fusing

Scientists at the Institute of Cancer Research in London and Linköping University in Sweden have discovered how cells prevent their chromosomes from mistakenly fusing together. Two proteins, TRF2 and RAP1, work together to block a repair process that would otherwise treat the natural ends of chromosomes as broken DNA and try to fix them.

Formation of the TRF2–RAP1–DNA-PK complex prevents unwanted chromosome fusions and helps explain how mammalian cells maintain individual linear chromosomes. Without this “brake,” whole chromosomes would stick end‑to‑end.

Each chromosome ends in a region called a telomere. These act like protective caps, often compared to the plastic tips on shoelaces, helping cells distinguish the natural ends of DNA from actual damage. When DNA breaks in other parts of the genome, a repair process called non-homologous end joining, or NHEJ, kicks in to rejoin the pieces.

One of the main enzymes involved is DNA-PK, which attracts other repair proteins to seal the break. But at telomeres, this same repair system must be kept away, or it could cause dangerous chromosome fusions.

Previous research has shown that a protein, TRF2, helps form a loop at the end of the chromosome, tucking the telomere in on itself to make it less visible to repair machinery. Another protein, called Apollo, helps disguise the telomere in a way that keeps it from being recognized as broken DNA. Even without Apollo and its overhang, DNA‑PK still fails to launch the usual, LIG4‑driven repair, hinting at yet another safeguard.

The current research team turned their attention to RAP1, a protein found in many species that was known to be involved in telomeres but whose role in mammals wasn’t well understood. In yeast, RAP1 is known to block end-joining at chromosome tips. Could it be doing something similar in human cells?

In the study, “Chromosome end protection by RAP1-mediated inhibition of DNA-PK,” published in Nature, researchers performed a structural and biochemical study to determine how TRF2 and RAP1 suppress DNA-PK-mediated end-joining activity at telomeres.

To investigate RAP1’s function, the researchers used both mouse and human cells. They removed the genes for RAP1 and Apollo, separately and together, then looked at how the chromosomes responded. Advanced imaging tools were used to observe how RAP1 physically interacts with the proteins involved in DNA repair.

In mouse cells, about 15% of telomeres were fused when both proteins were missing. In human cells, the number was even higher, up to 30%. Damage depended on the repair enzyme DNA-PK, showing that the usual repair process was mistakenly being activated at the ends of chromosomes.

Additional imaging and molecular experiments revealed how RAP1 interacts with the repair system. RAP1 binds to DNA-PK in a way that physically blocks it from bringing in another key player, LIG4, which is necessary to complete the repair. Without LIG4, fusion fails at the final step.

Further experiments showed that when RAP1 is unable to bind DNA-PK, either because of mutations or because part of the protein is missing, it no longer protects telomeres and chromosomes begin to fuse. When the researchers restored RAP1’s ability to block LIG4, protection returned.

The discovery provides a detailed explanation of how chromosomes avoid being mistaken for broken DNA. RAP1 as a molecular gatekeeper mechanism solves a long-standing puzzle in telomere resilience.

A fail-safe like this may be crucial when other safeguards break down, especially in aging or stressed cells. Because RAP1’s role is conserved across many species, it may be an ancient defense mechanism—one that predates Apollo’s involvement in telomere protection. Apollo’s overhang pathway and RAP1’s plug act as a parallel safeguard strategy where chromosomes can fuse only if both systems fail.

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