Distinct Features of Ribonucleotides Within Genomic DNA in Aicardi-Goutières Syndrome Ortholog Mutants of

Overview

Journal iScience

Publisher Cell Press

Date 2024 Jun 13

PMID 38868188

Authors

Deepali L Kundnani

Taehwan Yang

Alli L Gombolay

Kuntal Mukherjee

Gary Newnam

Chance Meers

Ishika Verma

Kirti Chhatlani

Zeel H Mehta

Celine Mouawad

Francesca Storici

Affiliations

Soon will be listed here.

Abstract

Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast : -G42S and -K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of -G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.

References

Wagih O . ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics. 2017; 33(22):3645-3647. DOI: 10.1093/bioinformatics/btx469. View

Chon H, Sparks J, Rychlik M, Nowotny M, Burgers P, Crouch R . RNase H2 roles in genome integrity revealed by unlinking its activities. Nucleic Acids Res. 2013; 41(5):3130-43. PMC: 3597693. DOI: 10.1093/nar/gkt027. View

Sui Y, Epstein A, Dominska M, Zheng D, Petes T, Klein H . Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides. Nucleic Acids Res. 2022; 50(12):6890-6902. PMC: 9262587. DOI: 10.1093/nar/gkac536. View

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

Storici F, Bebenek K, Kunkel T, Gordenin D, Resnick M . RNA-templated DNA repair. Nature. 2007; 447(7142):338-41. PMC: 2121219. DOI: 10.1038/nature05720. View

Ashour M, Mosammaparast N . Mechanisms of damage tolerance and repair during DNA replication. Nucleic Acids Res. 2021; 49(6):3033-3047. PMC: 8034635. DOI: 10.1093/nar/gkab101. View

Bergstrom E, Huang M, Mahto U, Barnes M, Stratton M, Rozen S . SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics. 2019; 20(1):685. PMC: 6717374. DOI: 10.1186/s12864-019-6041-2. View

Wanrooij P, Engqvist M, Forslund J, Navarrete C, Nilsson A, Sedman J . Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired. Proc Natl Acad Sci U S A. 2017; 114(47):12466-12471. PMC: 5703314. DOI: 10.1073/pnas.1713085114. View

Rohman M, Koga Y, Takano K, Chon H, Crouch R, Kanaya S . Effect of the disease-causing mutations identified in human ribonuclease (RNase) H2 on the activities and stabilities of yeast RNase H2 and archaeal RNase HII. FEBS J. 2008; 275(19):4836-49. PMC: 3178050. DOI: 10.1111/j.1742-4658.2008.06622.x. View

10.

Uehara R, Cerritelli S, Hasin N, Sakhuja K, London M, Iranzo J . Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development. Cell Rep. 2018; 25(5):1135-1145.e5. PMC: 6309994. DOI: 10.1016/j.celrep.2018.10.019. View

11.

Potenski C, Klein H . How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells. Nucleic Acids Res. 2014; 42(16):10226-34. PMC: 4176331. DOI: 10.1093/nar/gku773. View

12.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

13.

Hiller B, Hoppe A, Haase C, Hiller C, Schubert N, Muller W . Ribonucleotide Excision Repair Is Essential to Prevent Squamous Cell Carcinoma of the Skin. Cancer Res. 2018; 78(20):5917-5926. PMC: 6526525. DOI: 10.1158/0008-5472.CAN-18-1099. View

14.

Langmead B, Wilks C, Antonescu V, Charles R . Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics. 2018; 35(3):421-432. PMC: 6361242. DOI: 10.1093/bioinformatics/bty648. View

15.

Reijns M, Bubeck D, Gibson L, Graham S, Baillie G, Jones E . The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease. J Biol Chem. 2010; 286(12):10530-9. PMC: 3060506. DOI: 10.1074/jbc.M110.177394. View

16.

Zhang L, Yang Y, Cheng L, Cheng Y, Zhou H, Tan Z . Identification of Common Genes Refers to Colorectal Carcinogenesis with Paired Cancer and Noncancer Samples. Dis Markers. 2018; 2018:3452739. PMC: 5830953. DOI: 10.1155/2018/3452739. View

17.

Balachander S, Yang T, Newnam G, El-Sayed W, Koh K, Storici F . Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq. Methods Mol Biol. 2019; 2049:17-37. PMC: 9451030. DOI: 10.1007/978-1-4939-9736-7_2. View

18.

Koyanagi E, Kakimoto Y, Minamisawa T, Yoshifuji F, Natsume T, Higashitani A . Global landscape of replicative DNA polymerase usage in the human genome. Nat Commun. 2022; 13(1):7221. PMC: 9700718. DOI: 10.1038/s41467-022-34929-8. View

19.

Williams K, Lee M, Hu Y, Andreas J, Patel S, Zhang S . A systems genetics approach identifies CXCL14, ITGAX, and LPCAT2 as novel aggressive prostate cancer susceptibility genes. PLoS Genet. 2014; 10(11):e1004809. PMC: 4238980. DOI: 10.1371/journal.pgen.1004809. View

20.

Zhou Z, Williams J, Lujan S, Kunkel T . Ribonucleotide incorporation into DNA during DNA replication and its consequences. Crit Rev Biochem Mol Biol. 2021; 56(1):109-124. PMC: 7936655. DOI: 10.1080/10409238.2020.1869175. View