Malfatti, M. C. | Search bioRxiv

bioRxiv2025

Apurinic/apyrimidinic endodeoxyribonuclease 1 contributes to the repair of damaged intercalated-motif of telomeric sequences

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 their integrity. The complementary cytosine-rich strand forms another structure, the i-motif (iM), essential for telomere maintenance, though its repair mechanism remains unclear. Herein we investigate 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. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/694817v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1962c63org.highwire.dtl.DTLVardef@3c3f60org.highwire.dtl.DTLVardef@164d78borg.highwire.dtl.DTLVardef@1831aae_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

The Apurinic/Apyrimidinic Endodeoxyribonuclease 1 is an RNA G-quadruplex binding protein and regulates miR-92b expression in cancer cells

In the last decade, several novel functions of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) have been discovered, going far beyond its canonical function as a DNA repair enzyme, unveiling its potential roles in cancer development. Indeed, it was shown to be involved in DNA G-quadruplex biology and RNA metabolism, most importantly in the miRNA maturation pathway and the decay of oxidized- or abasic-miRNAs during oxidative stress conditions. Furthermore, in recent years several non-canonical pathways of miRNA biogenesis have been described, with a specific focus on guanosine-rich precursors that can form RNA G-quadruplex (rG4) structures. In this study, we show that several miRNA precursors, dysregulated upon APE1-depletion, contain an rG4 motif and that their corresponding target genes are upregulated after APE1-depletion. We also show, both by in vitro assays and by using a HeLa cell model, that APE1 can bind and regulate the folding of an rG4 structure contained in pre-miR92b, with a mechanism strictly dependent on critical lysine residues present in the N-terminal disordered region. Furthermore, APE1 depletion in HeLa cells alters the maturation process of miR-92b, mainly affecting the shuttling between the nucleus and cytosol. Lastly, bioinformatic analysis of APE1-regulated rG4-containing miRNAs supports the relevance of our findings for cancer biology. Specifically, these miRNAs exhibit high prognostic significance in lung, cervical, and liver cancer, as suggested by their involvement in several cancer-related pathways. Significance StatementWe highlight an undescribed non-canonical role of the mammalian Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) in the context of RNA G-quadruplexes (rG4), specifically in the alternative pathway of miRNA maturation of guanosine-rich miRNA precursors. Specifically, APE1 binds these structures and modulates their folding, mainly through its N-terminal region and some residues in its catalytic domain. Moreover, we showed an interesting new role of APE1 in regulating the shuttling and accumulation of miR-92b between the nuclear and cytosolic compartments, opening new perspectives on how APE1 may exercise its role in the miRNA maturation pathway and function. Moreover, APE1-depleted dysregulated miRNAs with rG4 motifs in their precursors have significant prognostic value in lung, cervical, and liver tumors, suggesting potential targets for cancer therapy.

molecular biology↗