In this study, Barry et al. uncover the mechanism by which Rap1—a conserved telomere binding protein that also has been implicated in activation of the NF-κB signaling pathway, maintenance of metabolic function in vivo, and transcriptional regulation—modulates gene expression. Using a separation-of-function allele, they show that Rap1 transcriptional regulation is largely independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci.