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.
Highlights
Among the many scientific contributions that Miro Radman has made to our understanding of genome biology, his work on the SOS response and mismatch repair stands out amongst the most visionary
The insertion of rNMPs in the genome enhances DNA reactivity, favors alkali cleavage, and causes backbone distortions, with possible repercussions on DNA-related transactions, such as replication and chromatin assembly [24]. In view of their potentially deleterious effects, genome-embedded rNMPs are efficiently removed by ribonucleotide excision repair (RER), an error-free pathway that relies on ribonucleotide recognition and excision by RNase H2, which removes the RNA stretches generated by primase activity [24]
Ribonucleotide incorporation by Pol μ favors the action of DNA ligase 4, which tolerates mispairs or gaps in the opposite strand, yet in this case prefers a terminal ribonucleotide [29]. Another DNA repair pathway that reportedly uses embedded ribonucleotides is mismatch repair (MMR), which is critical to correct nucleotide misincorporations that occur during replication
Summary
Among the many scientific contributions that Miro Radman has made to our understanding of genome biology, his work on the SOS response and mismatch repair stands out amongst the most visionary. We review evidence obtained from in vivo studies in light of findings arising from in vitro experiments and summarize: (i) how cellular enzymes involved in DNA metabolism recognize, utilize or tolerate RNA-containing substrates, and (ii) how this subof 16 strate promiscuity can either trigger the generation of genotoxic structures, or impact 2their repair. RNMP insertion represents a major error that occurs during DNA replication, which a steric-gate residueby favoring dNTP selection their nucleotide binding pocket, can has been confirmed genome-wide mappingat[23]. Even with rNMP incorporation disfavored, the high cellular concentration of rNTPs compared to dNTPs results in rates of ribonucleotide misincorporation within nascent DNA from ~1:600 to ~1:5000 depending on the DNA polymerase considered [11,22]. RNMP insertion represents a major error that occurs during DNA replication, which has been confirmed by genome-wide mapping [23]
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