Mutagenic Processing of Ribonucleotides in DNA by Yeast Topoisomerase I

Kim, Nayun; Huang, Shar Yin N.; Williams, Jessica S.; Li, Yue C.; Clark, Allan; Cho, Jang Eun; Kunkel, Thomas A.; Pommier, ﻿Yves; Jinks-Robertson, Sue

doi:10.1126/science.1205016

Cited by 252 publications

(383 citation statements)

References 25 publications

Supporting

Mentioning

365

Contrasting

Order By: Relevance

“…As originally proposed in the model for Top1 cleavage at rNMPs in DNA, 2,10 we have shown that the ligation activity of Top1 is needed to induce slippage mutations. In vitro studies have provided evidence for a role of Tdp1 in the ribonucleotide-induced lesions by processing the Top1-cc.…”

Section: Discussionmentioning

confidence: 96%

“…the intact DNA strand and ligation to the 5 0 -OH end. 2 This reaction has been reconstituted in vitro. 12,13 These studies also revealed that the second Top1 cleavage 2 nucleotides from the cyclic 2 0 -3 0 phosphate led to a covalent Top1-cleavage complex (Top1-cc).…”

Section: Roles Of Top1 and Tdp1 In Cleavage And Processing At An Rnmpmentioning

confidence: 99%

“…To identify other nucleases that could be involved in processing rNMP-induced DNA nicks, we surveyed 7 additional nucleases that have a known role in DNA replication and/or repair in rnh202 cells, using a dinucleotide repeat hotspot reporter for slippage mutation that is suited to assessing rNMP-mediated mutagenesis 1,2 (Fig. 1).…”

Section: Dna Repair Nucleasesmentioning

confidence: 99%

“…9 There is good evidence that Top1-mediated nicks at rNMP residues act as the initiating DNA lesion in slippage mutation induction. 1,2,10,11 To determine the linkage of the ligation step to mutations, we used the dinucleotide slippage reporter to examine the effect of the top1-T722A allele on mutation rates. As shown in Figure 2A, top1-T722A behaves identically to the null allele, thus showing that both rNMP cleavage and DNA ligation are needed to generate the necessary lesion for mutation induction.…”

Section: Roles Of Top1 and Tdp1 In Cleavage And Processing At An Rnmpmentioning

confidence: 99%

“…1,2,18 For the (AG) 4 slippage reporter, single colonies were inoculated into 5 mL YPD and grown for 2 d at 30 C, washed and resuspended in 1 mL H 2 O. Cells were plated onto SC-lysine medium to select for slippage mutants and onto SC medium for total cell number.…”

Section: Determination Of Mutation Ratesmentioning

confidence: 99%

See 4 more Smart Citations

Roles of DNA helicases and Exo1 in the avoidance of mutations induced by Top1-mediated cleavage at ribonucleotides in DNA

et al. 2016

View full text Add to dashboard Cite

The replicative DNA polymerases insert ribonucleotides into DNA at a frequency of approximately 1/6500 nucleotides replicated. The rNMP residues make the DNA backbone more susceptible to hydrolysis and can also distort the helix, impeding the transcription and replication machineries. rNMPs in DNA are efficiently removed by RNaseH2 by a process called ribonucleotides excision repair (RER). In the absence of functional RNaseH2, rNMPs are subject to cleavage by Topoisomerase I, followed by further processing to result in deletion mutations due to slippage in simple DNA repeats. The topoisomerase I-mediated cleavage at rNMPs results in DNA ends that cannot be ligated by DNA ligase I, a 5 0 OH end and a 2 0 -3 0 cyclic phosphate end. In the budding yeast, the mutation level in RNaseH2 deficient cells is kept low via the action of the Srs2 helicase and the Exo1 nuclease, which collaborate to process the Top1-induced nick with subsequent non-mutagenic gap filling. We have surveyed other helicases and nucleases for a possible role in reducing mutagenesis at Top1 nicks at rNMPs and have uncovered a novel role for the RecQ family helicase Sgs1 in this process.

show abstract

Section: Discussionmentioning

confidence: 96%

Section: Roles Of Top1 and Tdp1 In Cleavage And Processing At An Rnmpmentioning

confidence: 99%

Section: Dna Repair Nucleasesmentioning

confidence: 99%

Section: Roles Of Top1 and Tdp1 In Cleavage And Processing At An Rnmpmentioning

confidence: 99%

Section: Determination Of Mutation Ratesmentioning

confidence: 99%

See 3 more Smart Citations

Roles of DNA helicases and Exo1 in the avoidance of mutations induced by Top1-mediated cleavage at ribonucleotides in DNA

et al. 2016

View full text Add to dashboard Cite

show abstract

Ribonucleotides in mitochondrial DNA

Wanrooij

Chabes

2019

FEBS Letters

View full text Add to dashboard Cite

The incorporation of ribonucleotides (rNMPs) into DNA during genome replication has gained substantial attention in recent years and has been shown to be a significant source of genomic instability. Studies in yeast and mammals have shown that the two genomes, the nuclear DNA (nDNA) and the mitochondrial DNA (mtDNA), differ with regard to their rNMP content. This is largely due to differences in rNMP repair – whereas rNMPs are efficiently removed from the nuclear genome, mitochondria lack robust mechanisms for removal of single rNMPs incorporated during DNA replication. In this minireview, we describe the processes that determine the frequency of rNMPs in the mitochondrial genome and summarise recent findings regarding the effect of incorporated rNMPs on mtDNA stability and function.

show abstract

Structural Impact of Single Ribonucleotide Residues in DNA

et al. 2016

View full text Add to dashboard Cite

Single ribonucleotide intrusions represent the most common nonstandard nucleotide type found incorporated in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA. To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts-AxC, CxG, and GxC, where x=rG or dG-we report the structures of three single-ribonucleotide-containing DNA duplexes and the corresponding DNA controls. The lesion subtly and locally perturbs the structure asymmetrically on the 3' side of the lesion in both the riboguanosine-containing and the complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3'-downstream deoxyribose units are predominately in N-type conformation; backbone torsion angles ϵ and/or ζ of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'-neighboring base, and/or sugar. Interestingly, even in similar purine-rG-pyrimidine environments (A-rG-C and G-rG-C), a riboguanosine unit affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.

show abstract

Mutagenic Processing of Ribonucleotides in DNA by Yeast Topoisomerase I

Cited by 252 publications

References 25 publications

Roles of DNA helicases and Exo1 in the avoidance of mutations induced by Top1-mediated cleavage at ribonucleotides in DNA

Roles of DNA helicases and Exo1 in the avoidance of mutations induced by Top1-mediated cleavage at ribonucleotides in DNA

Ribonucleotides in mitochondrial DNA

Structural Impact of Single Ribonucleotide Residues in DNA

Contact Info

Product

Resources

About