Rloops

R-loops are three-stranded nucleic acid structures that form during transcription when the nascent RNA re-anneals to the DNA template strand, creating a DNA:RNA hybrid and displacing the non-template DNA strand. The resulting structure consists of an RNA–DNA hybrid accompanying a looped, single-stranded DNA region. R-loops occur in both bacteria and eukaryotes and are most common in regions of high transcriptional activity, GC-rich sequences, or genomic contexts that favor hybrid stability.

Formation and regulation of R-loops are influenced by transcription dynamics and chromatin context. They can arise co-transcriptionally when the RNA transcript folds back and invades the DNA duplex. Enzymes such as RNase H, which specifically degrades RNA in RNA–DNA hybrids, act to remove or prevent R-loops. Helicases and other RNA/DNA unwinding factors (for example, Senataxin) help resolve existing structures. Topoisomerases reduce supercoiling that promotes hybrid formation, and chromatin remodelers can modulate accessibility and stability of R-loops.

Biological significance varies by organism and genomic locus. R-loops can participate in normal processes such as transcription termination and immune system diversification in B cells, and may regulate gene expression under certain conditions. However, accumulation of R-loops can threaten genome integrity by blocking replication forks, provoking replication stress, and triggering DNA damage responses. Such accumulation is associated with genome instability and has been linked to diseases including BRCA1/BRCA2-related cancers, Fanconi anemia, and some neurodegenerative disorders.

Detection and study commonly use antibodies that recognize RNA–DNA hybrids, notably in methods like DRIP and DRIP-seq. Validation often involves RNase H treatment to confirm hybrid-specific signals. Ongoing research seeks to map locus-specific dynamics and to understand how cells balance R-loop formation with genome maintenance.