R-loops processing by human apurinic/apyrimidinic endonuclease APE1

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• R-loops are nucleic acid structures formed during transcription.
• Unscheduled R-loop accumulation can cause genomic instability.
• Apurinic/apyrimidinic endonuclease 1 (APE1) is primarily known for DNA repair.

Purpose of the Study:

• To investigate the in vitro enzymatic processing of R-loops by APE1.
• To explore APE1's RNase H and AP-endonuclease activities on R-loop structures.
• To understand APE1's role in nucleic acid metabolism beyond DNA repair.

Main Methods:

• In vitro enzymatic assays using R-loop substrates.
• Analysis of APE1's RNase H activity on DNA:RNA hybrids of varying lengths.
• Assessment of APE1's AP-endonuclease activity on abasic sites within R-loops.

Main Results:

• APE1 exhibits RNase H activity on DNA:RNA hybrids in R-loops, decreasing with hybrid length >16 nucleotides.
• APE1 cleaves abasic sites in both RNA and DNA strands of R-loops.
• Processing of abasic sites in RNA is followed by exoribonuclease degradation; abasic sites in DNA inhibit RNase H activity.

Conclusions:

• APE1 possesses versatile enzymatic activities (RNase H, AP-endonuclease, exoribonuclease) that process R-loops.
• APE1's processing of R-loops contributes to nucleic acid metabolism and genome regulation.
• This study expands the known biological significance of APE1 beyond its canonical DNA repair functions.