TERRA R-loops trigger a switch in telomere maintenance towards break-induced replication and PrimPol-dependent repair

TERRA long noncoding RNAs associate with telomeres post transcription through base-pairing with telomeric DNA forming R-loop structures. TERRA regulates telomere maintenance but its exact modes of action remain unknown. Here, we induce TERRA transcription and R-loop formation in telomerase-expressing cells and determine that TERRA R-loop formation requires non-redundant functions of the RAD51 DNA recombinase and its enhancer RAD51AP1. TERRA R-loops interfere with semiconservative DNA replication promoting telomere maintenance by a homology-directed repair (HDR) mechanism known as Break Induced Replication (BIR), which ensures telomere maintenance in ALT cancer cells. In addition, TERRA induced PrimPol-dependent repair, which can initiate DNA synthesis de novo downstream of replication obstacles. PrimPol acts in parallel to BIR for telomere maintenance of TERRA over-expressing cells promoting their survival. Similarly, we find that PrimPol depletion is synthetic lethal with BIR deficiency in U2OS ALT cancer cells. Therefore, in the absence of other ALT-typical telomeric chromatin changes, TERRA R-loops per se are sufficient to induce ALT-typical telomere repair mechanisms.