A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

• Published in: Nucleic acids research Vol. 40; no. 20; pp. 10334 - 10344
• Main Authors: Wanrooij, Paulina H, Uhler, Jay P, Shi, Yonghong, Westerlund, Fredrik, Falkenberg, Maria, Gustafsson, Claes M
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.11.2012
• Subjects: binding protein; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; Circular Dichroism; Conserved sequence; Data processing; DNA biosynthesis; DNA Replication; DNA, Mitochondrial - biosynthesis; DNA, Mitochondrial - chemistry; formation; G-Quadruplexes; Genome Integrity, Repair and; human pif1 helicase; Humans; Hybrids; in-vitro; Lead; Medicin och hälsovetenskap; Mitochondria; Mitochondrial DNA; polymerase; primer; Primers; R-loops; Replication; Replication initiation; Replication origins; RNA; RNA - chemistry; sequence; strand origin; Transcription termination; Transcription Termination, Genetic; Transcription, Genetic; twinkle
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gks802

In human mitochondria the transcription machinery generates the RNA primers needed for initiation of DNA replication. A critical feature of the leading-strand origin of mitochondrial DNA replication is a CG-rich element denoted conserved sequence block II (CSB II). During transcription of CSB II, a G-quadruplex structure forms in the nascent RNA, which stimulates transcription termination and primer formation. Previous studies have shown that the newly synthesized primers form a stable and persistent RNA-DNA hybrid, a R-loop, near the leading-strand origin of DNA replication. We here demonstrate that the unusual behavior of the RNA primer is explained by the formation of a stable G-quadruplex structure, involving the CSB II region in both the nascent RNA and the non-template DNA strand. Based on our data, we suggest that G-quadruplex formation between nascent RNA and the non-template DNA strand may be a regulated event, which decides the fate of RNA primers and ultimately the rate of initiation of DNA synthesis in human mitochondria.