The single-stranded telomeric DNA binding protein POT1 protects mammalian chromosome ends from the ATR-dependent DNA damage response, regulates telomerase-mediated telomere extension, and limits 5-end resection at telomere termini. Whereas most mammals have a single POT1 gene, mice have two POT1 proteins that are functionally distinct. POT1a represses the DNA damage response, and POT1b controls 5-end resection. In contrast, as we report here, POT1a and POT1b do not differ in their ability to repress telomere recombination. By swapping domains, we show that the DNA binding domain of POT1a specifies its ability to repress the DNA damage response. However, no differences were detected in the in vitro DNA binding features of POT1a and POT1b. In contrast to the repression of ATR signaling by POT1a, the ability of POT1b to control 5-end resection was found to require two regions in the C terminus, one corresponding to the TPP1 binding domain and a second representing a new domain located between amino acids (aa) 300 and 350. Interestingly, the DNA binding domain of human POT1 can replace that of POT1a to repress ATR signaling, and the POT1b region from aa 300 to 350 required for the regulation of the telomere terminus is functionally conserved in human POT1. Thus, human POT1 combines the features of POT1a and POT1b.Mammalian chromosome ends associate with shelterin, the protein complex dedicated to telomere protection and homeostasis (reviewed in references 5 and 20). The DNA of mammalian telomeres consists of long arrays of doublestranded (ds) TTAGGG repeats ending in a single-stranded (ss) protrusion of the 3Ј end, referred to as the 3Ј overhang. The 3Ј-overhang strand can invade the duplex part of telomeres, forming a lariat structure called the t-loop (8). Three shelterin components interact with telomeric DNA. POT1 recognizes ss TTAGGG repeats and therefore can associate with the telomeric 3Ј overhang as well as with the displaced strand at the base of the t-loop. TRF1 and TRF2 cover the duplex part of telomeric DNA, and they recruit the other shelterin components Rap1, TIN2, and TPP1 to telomeres through protein-protein interactions. POT1 cannot localize to telomeres alone but instead requires heterodimerization with TPP1; this interaction is crucial for the association of POT1 with telomeres, as TPP1 tethers POT1 to TRF1 and TRF2 by a TPP1-TIN2 bridge and improves the DNA binding affinity of POT1 (12,19,26).Shelterin masks telomeres from the cellular machinery that recognizes and repairs DNA lesions. If shelterin function is perturbed, DNA damage response factors accumulate at telomeres, leading to the activation of the ATM and ATR kinase signaling pathways (2, 10, 15, 29). Distinct components of shelterin independently repress ATM and ATR signaling: TRF2 is required to prevent ATM activation at telomeres, while POT1 represses the activation of ATR (16). Dysfunctional telomeres trigger various DNA repair reactions and can be processed like dsDNA breaks through nonhomologous end joining or through homology-direc...