APE1 binds and processes abasic sites present in i-motif DNA and cooperates with PCBP1 in maintenance of telomeric...

Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is a key enzyme in the base excision repair pathway, responsible for processing abasic (AP) sites. Recent studies revealed that APE1 participates in repairing DNA secondary structures as G-quadruplexes (G4). Telomeres, stabilized by shelterin proteins, are rich in G4, where APE1 binds and repairs AP-sites to maintain telomere integrity. The G4-complementary, cytosine-rich strand forms the i-motif (iM) structure, essential for telomere maintenance, though its repair mechanism remains unclear. Herein, we investigated APE1 binding and processing capabilities toward native and damaged telomeric iM, bearing AP-sites in different positions. Using biochemical and biophysical assays, we found that APE1 binds the telomeric iM sequence and that its cleavage efficiency depends on AP-site position within iM. Proximity ligation assay analysis, in HeLa and U2OS cells, highlighted a novel interaction between APE1 and PCBP1, a well-known iM-folding modulator. PCBP1 binds iM with higher affinity than APE1 and inhibits its cleavage activity on damaged iM. Immunofluorescence and telomere restriction fragment analyses showed that depletion of APE1 or PCBP1 impairs their interaction with the shelterin components, affecting telomere length. These results connect APE1 canonical DNA repair activity with the maintenance of non-canonical DNA secondary structures in telomeres, through its interaction with PCBP1.