Rap1-mediated steric hindrance protects telomeres from MRX sensing

Telomere capping largely depends on telomere length. Abnormally short telomeres are prone to activate DNA damage checkpoint, undergo unscheduled chromosomal fusions through nonhomologous end-joining (NHEJ) and be resected. All these processes are mediated by the Mre11–Rad50–Xrs2NBS1 (MRXMRN) complex. The response to telomere length is thought to correlate with the number of DNA-bound telomeric proteins but the mechanisms translating this number into functional protection remain unclear. Here, combining genetic and reconstitution biochemistry approaches, we explain why NHEJ inhibition and DNA resection suppression are proportional to the length of Rap1-bound arrays adjacent to DNA ends in Saccharomyces cerevisiae. Our findings reveal that MRX has a capacity to distinguish short from long protein blocks at DNA breaks, which translates into the ability of Rap1 protein–DNA arrays to suppress MRX on the basis of their length. Unlike the previously described direct inhibition of MRXMRN by Rif2 and TRF2 iDDR, the process described here does not rely on direct protein–protein interactions. Instead, Rap1 inhibits MRX by steric hindrance, determined both by the length of DNA it shields and by the coverage density. These results explain how cells detect short telomeres, a crucial process for telomere length homeostasis and telomere-driven senescence. The authors show that Rap1 protein coverage protects telomeres by physically blocking the Mre11–Rad50–Xrs2NBS1 complex. Longer, denser Rap1 arrays better prevent DNA damage responses, providing a mechanism for how cells detect short telomeres and maintain genome stability