Direct, Genome-wide Assessment of DNA Mutations in Single Cells

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Nov 17

PMID 22086961

Citations 51

Authors

Michael Gundry

Wenge Li

Shahina Bano Maqbool

Jan Vijg

Affiliations

Soon will be listed here.

Abstract

DNA mutations are the inevitable consequences of errors that arise during replication and repair of DNA damage. Because of their random and infrequent occurrence, quantification and characterization of DNA mutations in the genome of somatic cells has been difficult. Random, low-abundance mutations are currently inaccessible by standard high-throughput sequencing approaches because they cannot be distinguished from sequencing errors. One way to circumvent this problem and simultaneously account for the mutational heterogeneity within tissues is whole genome sequencing of a representative number of single cells. Here, we show elevated mutation levels in single cells from Drosophila melanogaster S2 and mouse embryonic fibroblast populations after treatment with the powerful mutagen N-ethyl-N-nitrosourea. This method can be applied as a direct measure of exposure to mutagenic agents and for assessing genotypic heterogeneity within tissues or cell populations.

Citing Articles

Concurrent analysis of genome and transcriptome in one single cell.

Heid J, Cutler R, Lee M, Vijg J, Maslov A BMC Res Notes. 2024; 17(1):267.

PMID: 39285281 PMC: 11403997. DOI: 10.1186/s13104-024-06927-0.

Methods and applications of genome-wide profiling of DNA damage and rare mutations.

Pfeifer G, Jin S Nat Rev Genet. 2024; 25(12):846-863.

PMID: 38918545 PMC: 11563917. DOI: 10.1038/s41576-024-00748-4.

Somatic mutations in aging and disease.

Ren P, Zhang J, Vijg J Geroscience. 2024; 46(5):5171-5189.

PMID: 38488948 PMC: 11336144. DOI: 10.1007/s11357-024-01113-3.

Analyzing somatic mutations by single-cell whole-genome sequencing.

Zhang L, Lee M, Maslov A, Montagna C, Vijg J, Dong X Nat Protoc. 2023; 19(2):487-516.

PMID: 37996541 PMC: 11406548. DOI: 10.1038/s41596-023-00914-8.

Somatic mutation burden in relation to aging and functional life span: implications for cellular reprogramming and rejuvenation.

Maslov A, Vijg J Curr Opin Genet Dev. 2023; 83:102132.

PMID: 37931583 PMC: 10841402. DOI: 10.1016/j.gde.2023.102132.

References

Quail M, Kozarewa I, Smith F, Scally A, Stephens P, Durbin R . A large genome center's improvements to the Illumina sequencing system. Nat Methods. 2008; 5(12):1005-10. PMC: 2610436. DOI: 10.1038/nmeth.1270. View

Quail M, Swerdlow H, Turner D . Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet. 2009; Chapter 18:Unit 18.2. PMC: 3849550. DOI: 10.1002/0471142905.hg1802s62. View

Busuttil R, Rubio M, Dolle M, Campisi J, Vijg J . Oxygen accelerates the accumulation of mutations during the senescence and immortalization of murine cells in culture. Aging Cell. 2003; 2(6):287-94. DOI: 10.1046/j.1474-9728.2003.00066.x. View

Bielas J, Heddle J . Proliferation is necessary for both repair and mutation in transgenic mouse cells. Proc Natl Acad Sci U S A. 2000; 97(21):11391-6. PMC: 17210. DOI: 10.1073/pnas.190330997. View

Fox E, Salk J, Loeb L . Cancer genome sequencing--an interim analysis. Cancer Res. 2009; 69(12):4948-50. PMC: 2699895. DOI: 10.1158/0008-5472.CAN-09-1231. View

DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C . A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43(5):491-8. PMC: 3083463. DOI: 10.1038/ng.806. View

Op het Veld C, van Zeeland A, Jansen J . Effect of nucleotide excision repair on hprt gene mutations in rodent cells exposed to DNA ethylating agents. Mutagenesis. 1997; 12(6):417-24. DOI: 10.1093/mutage/12.6.417. View

Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B . Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 2009; 20(2):155-69. PMC: 2813472. DOI: 10.1101/gr.099796.109. View

Kalisky T, Quake S . Single-cell genomics. Nat Methods. 2011; 8(4):311-4. DOI: 10.1038/nmeth0411-311. View

10.

Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander E, Getz G . Integrative genomics viewer. Nat Biotechnol. 2011; 29(1):24-6. PMC: 3346182. DOI: 10.1038/nbt.1754. View

11.

Geigl J, Speicher M . Single-cell isolation from cell suspensions and whole genome amplification from single cells to provide templates for CGH analysis. Nat Protoc. 2007; 2(12):3173-84. DOI: 10.1038/nprot.2007.476. View

12.

Druley T, Vallania F, Wegner D, Varley K, Knowles O, Bonds J . Quantification of rare allelic variants from pooled genomic DNA. Nat Methods. 2009; 6(4):263-5. PMC: 2776647. DOI: 10.1038/nmeth.1307. View

13.

Dear P . One by one: Single molecule tools for genomics. Brief Funct Genomic Proteomic. 2004; 1(4):397-416. DOI: 10.1093/bfgp/1.4.397. View

14.

Mahabir A, Zwart E, Schaap M, van Benthem J, de Vries A, Hernandez L . lacZ mouse embryonic fibroblasts detect both clastogens and mutagens. Mutat Res. 2009; 666(1-2):50-6. DOI: 10.1016/j.mrfmmm.2009.04.005. View

15.

Gore A, Li Z, Fung H, Young J, Agarwal S, Antosiewicz-Bourget J . Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011; 471(7336):63-7. PMC: 3074107. DOI: 10.1038/nature09805. View

16.

Zhang Y, Malone J, Powell S, Periwal V, Spana E, MacAlpine D . Expression in aneuploid Drosophila S2 cells. PLoS Biol. 2010; 8(2):e1000320. PMC: 2826376. DOI: 10.1371/journal.pbio.1000320. View

17.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

18.

Sekelsky J, Brodsky M, Burtis K . DNA repair in Drosophila: insights from the Drosophila genome sequence. J Cell Biol. 2000; 150(2):F31-6. PMC: 2180214. DOI: 10.1083/jcb.150.2.f31. View

19.

Campbell P, Stephens P, Pleasance E, OMeara S, Li H, Santarius T . Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008; 40(6):722-9. PMC: 2705838. DOI: 10.1038/ng.128. View

20.

Ohi Y, Qin H, Hong C, Blouin L, Polo J, Guo T . Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011; 13(5):541-9. PMC: 3987913. DOI: 10.1038/ncb2239. View