Detection of R-Loops by In Vivo and In Vitro Cytosine Deamination in Saccharomyces cerevisiae

R-loops are transcriptional by-products formed by a hybrid of the nascent RNA molecule with its DNA template and the displaced nontemplate DNA strand. The single stranded nature of the displaced nontemplate strand makes it vulnerable to attack. This property is used in nature to cause directed mutagenesis and breaks by the action of the activation-induced cytosine deaminase (AID) enzyme and can thus be exploited to detect the presence of R-loops even when they form at low frequencies by overexpressing this enzyme in vivo or by in vitro treatment with the bisulfite anion, which further allows nucleotide resolution. This is of particular relevance given the fact that R-loops have the potential to hamper DNA replication and repair, threatening genome integrity. Here, we describe the protocols used in the yeast Saccharomyces cerevisiae to infer the presence of R-loops through increased AID-induced DNA damage, measured as increased recombination or Rad52 foci formation as well as to detect single R-loop molecules and determine their length at particular genomic sites via bisulfite treatment and amplification.

A new interaction between BRCA2 and DDX5 promotes the repair of DNA breaks at transcribed chromatin

In a recent report, we have revealed a new interaction between the BRCA2 DNA repair associated protein (BRCA2) and the DEAD-box helicase 5 (DDX5) at DNA breaks that promotes unwinding DNA-RNA hybrids within transcribed chromatin and favors repair. Interestingly, BRCA2-DDX5 interaction is impaired in cells expressing the BRCA2^{T2 07A} missense variant found in breast cancer patients.

The role of R-loops in transcription-associated DNA double-strand break repair

The roles of RNA in the DNA damage response are emerging. We highlight findings from our recent study demonstrating the mechanism for transcription-associated homologous recombination repair (TA-HRR) of DNA double-strand breaks and the critical role of R-loops in TA-HRR.