The Ultimate (Mis)match: When DNA Meets RNA

Abstract

RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.

Keywords: DNA repair; DNA:RNA hybrid; R-loop; RNA; genetic recombination; genetic stability; ribonucleotide; transcription.

Figure 1

The variety of RNA-containing structures in the genome. Different types of ribonucleotide- or RNA-containing structures are represented in orange. The enzymes with reported contributions to their generation or removal are listed in blue and magenta, respectively, and the repair pathways with which they are associated are italicized. The orange and grey arrows indicate the direction of RNA and DNA synthesis, respectively. RNAP, RNA polymerase. (a), Ribonucleotide incorporation during DNA replication. For simplicity, only one branch of the replication fork is represented. (b), R-loop formation and resolution. (c), DNA:RNA hybrid accumulation at DSBs. (d), RNA-templated DNA repair. The cDNA produced upon reverse-transcription can also be used in homology-directed repair in a Rad51- and Rad52-dependent process (not depicted). See text for details.

Figure 2

An overview of the enzymatic reactions engaging RNA-containing structures. Examples of enzymes reported to catalyze the indicated reactions are listed, and their respective substrates and products are represented for forward and inverse strand exchange (a,b), branch migration (c), RNA degradation (d) and DNA:RNA unwinding (e). Note that RNase H2 can also excise ribonucleotides and degrade short RNA primers embedded within the genome.