During the past several years, an increasing number of obstacles to DNA-related transactions was found to similarly trigger DNA repair and tolerance mechanisms. Among them, RNA-containing structures have recently caught the attention of DNA biologists. These range from single ribonucleotide insertions to RNA stretches, DNA:RNA hybrids and R-loops, in which a single-stranded DNA is displaced. Such structures are observed in diverse species and represent a significant fraction of their genomes: for example, ribonucleotides are incorporated in newly synthesized DNA at an overall rate of ~1:1000 nucleotides and R-loops occupy approximately 5% of the human genome. It has become increasingly clear that these structures are relevant for genome integrity: on the one hand, genetic screens have highlighted the importance of RNA metabolism factors in the DNA damage response, and on the other hand, factors classically associated with DNA repair or genome maintenance handle RNA-containing substrates in vitro.