Processing ribonucleotides incorporated during eukaryotic DNA replication

Abstract

Preface The information encoded in DNA is influenced by the presence of non-canonical nucleotides, the most frequent of which are ribonucleotides. In this review we discuss recent discoveries about ribonucleotide incorporation into DNA during replication by the three major eukaryotic replicases, DNA polymerases α, δ and ε. The presence of ribonucleotides in DNA causes short deletion mutations and may result in the generation of DNA single- and double-strand breaks, leading to genomic instability. We describe how these ribonucleotides are removed from DNA by ribonucleotide excision repair and by topoisomerase 1. We discuss the biological consequences and the physiological roles of ribonucleotides in DNA, and consider how deficiencies in their removal from DNA may be important in the etiology of disease.

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism

“…For comprehensive information of all DNA polymerases and for replication fork restart, readers are referred to the book “DNA polymerases” by Hübscher et al (24) and the review by K. Marians in this volume, respectively. Although beyond the scope of this review, resolving conflicts between replication and transcription (25) and removing ribonucleotides incorporated during replication and repair (26) are highly relevant to TLS and sGRS and should not be overlooked.…”

Genome integrity and disease prevention in the nervous system

“…The incorporation of rNTPs into DNA may be one of the most frequent mistakes that occur during DNA replication, with estimates suggesting that on the order of >1,000,000 rNTPs are incorporated during replication in a mammalian cell (Nick McElhinny et al 2010a;Wallace and Williams 2014;Cerritelli and Crouch 2016;Williams et al 2016Williams et al , 2017. In fact, this lesion may be the most common type of endogenous DNA damage encountered by a proliferating cell.…”

“…R loops have also been implicated in fragile X-associated tremor/ataxia syndrome, where they occur at the FMR1 locus and may affect gene function, leading to neuronal toxicity (Loomis et al 2014). RNase H1 and H2 are also important for R-loop resolution in addition to their roles in rNTP removal from DNA (Chon et al 2013;Amon and Koshland 2016;Williams et al 2016). Importantly, if a main physiologic function of SETX is R-loop resolution, then this implicates R loops as a major source of endogenous genomic damage in the nervous system.…”

“…The mismatch repair pathway can work in conjunction with DNA polymerases to remove both mismatched bases in DNA and also rNTP incorporation into DNA (Ghodgaonkar et al 2013;Lujan et al 2013). rNTP incorporation into DNA is problematic for DNA integrity, as the defining 2 ′ -OH moiety on the rNTP sugar is particularly reactive and can cause strand breaks via hydrolysis, generating an aberrant 5 ′ -OH end or nucleophilic attack forming a 2 ′ -3 ′ -cyclic phosphate (Williams et al 2016). Incorporated rNTPs can also promote helical distortions, which can be sensed as DNA damage (Wallace and Williams 2014).…”

“…1). Among these, rNTP incorporation into DNA, genome damage from transcription-associated R-loop formation (hybridization of nascent primary RNA transcripts to the transcribed DNA strand), and aberrant topoisomerase activity are potential threats to the neural genome (McKinnon 2016;Williams et al 2016).…”