Visualization and interpretation of eukaryotic DNA replication intermediates in vivo by electron microscopy

Methods in Molecular Biology

Volumn 1094, Issue , 2014, Pages 177-208

  Neelsen, Kai J ^a   Chaudhuri, Arnab Ray ^a   Follonier, Cindy ^a   Herrador, Raquel ^a   Lopes, Massimo ^a  

^a NONE

Author keywords

DNA replication; Electron microscopy; In vivo replication intermediates; Nucleosome occupancy; Psoralen cross linking; Replication fork reversal; ssDNA

Indexed keywords

GENOMIC DNA; CELL EXTRACT; CROSS LINKING REAGENT; CRUCIFORM DNA; DNA; PSORALEN;

ANIMAL CELL; CONTROLLED STUDY; DNA EXTRACTION; DNA REPLICATION; EGG EXTRACT; ELECTRON MICROSCOPY; IN VIVO STUDY; MALE; NONHUMAN; TRANSMISSION ELECTRON MICROSCOPY; XENOPUS; ANIMAL; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMATIN; CYTOLOGY; DNA DENATURATION; DRUG EFFECT; EUKARYOTIC CELL; FUNGAL GENOME; GENETICS; MAMMAL; METABOLISM; METHODOLOGY; SACCHAROMYCES CEREVISIAE; SPERMATOZOON; ULTRASTRUCTURE;

ANIMALS; CELL EXTRACTS; CHROMATIN; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CROSS-LINKING REAGENTS; DNA; DNA REPLICATION; DNA, CRUCIFORM; EUKARYOTIC CELLS; FICUSIN; GENOME, FUNGAL; MALE; MAMMALS; MICROSCOPY, ELECTRON; NUCLEIC ACID DENATURATION; SACCHAROMYCES CEREVISIAE; SPERMATOZOA; XENOPUS;

EID: 84888816884     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-706-8_15     Document Type: Chapter

References (23)

1. Inciarte MR, Salas M, Sogo JM (1980) Structure of replicating DNA molecules of Bacillus subtilis bacteriophage phi 29. J Virol 34:187–199.
2. Lucchini R, Sogo JM (1995) Replication of transcriptionally active chromatin. Nature 374:276–280.
3. Sogo JM et al (1986) Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J Mol Biol 189:189–204.
4. Avemann K et al (1988) Camptothecin, a specifi c inhibitor of type I DNA topoisomerase, induces DNA breakage at replication forks. Mol Cell Biol 8:3026–3034.
5. Berti M, Ray Chaudhuri A, Thangavel S et al (2013) Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nat Struct Mol Biol 20:347–354.
6. Engels K et al (2011) 14-3-3 Proteins regulate exonuclease 1-dependent processing of stalled replication forks. PLoS Genet 7:e1001367.
7. Follonier C, Oehler J, Herrador R et al (2013) Friedreich’s Ataxia associated GAA repeats induce replication fork reversal and unusual molecular junctions in human cells. Nat Struct Mol Biol 20:486–494.
8. Giannattasio M et al (2010) Exo1 competes with repair synthesis, converts NER intermediates to long ssDNA gaps, and promotes checkpoint activation. Mol Cell 40:50–62.
9. Hashimoto Y et al (2010) Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat Struct Mol Biol 17:1305–1311.
10. Lopes M, Foiani M, Sogo JM (2006) Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol Cell 21:15–27.
11. Mojas N, Lopes M, Jiricny J (2007) Mismatch repair-dependent processing of methylation damage gives rise to persistent single-stranded gaps in newly replicated DNA. Genes Dev 21:3342–3355.
12. Neelsen KJ, Zanini IMY, Herrador R et al (2013) Oncogenes induce genotoxic stress by mitotic processing of unusual replication intermediates. J Cell Biol 6:699–708.
13. Ray Chaudhuri A et al (2012) Topoisomerase I poisoning results in PARP-mediated replication fork reversal. Nat Struct Mol Biol 19:417–423.
14. Sogo JM, Lopes M, Foiani M (2002) Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297:599–602.
15. Lopes M (2009) Electron microscopy methods for studying in vivo DNA replication intermediates. Methods Mol Biol 521:605–631.
16. Gasser R, Koller T, Sogo JM (1996) The stability of nucleosomes at the replication fork. J Mol Biol 258:224–239.
17. Gruss C et al (1993) Disruption of the nucleosomes at the replication fork. EMBO J 12:4533–4545.
18. Wellinger RE et al (1999) In vivo mapping of nucleosomes using psoralen-DNA crosslinking and primer extension. Methods Mol Biol 119:161–173.
19. Gruber M, Wellinger RE, Sogo JM (2000) Architecture of the replication fork stalled at the 3′ end of yeast ribosomal genes. Mol Cell Biol 20:5777–5787.
20. Vollenweider HJ, Sogo JM, Koller T (1975) A routine method for protein-free spreading of double-and single-stranded nucleic acid molecules. Proc Nat Acad Sci USA 72:83–87.
21. Sogo JM, Thoma F (1989) Electron microscopy of chromatin. Methods Enzymol 170:142–165.
22. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. CSHL Press, New York, USA.
23. Trenz K, Errico A, Costanzo V (2008) Plx1 is required for chromosomal DNA replication under stressful conditions. EMBO J 27: 876–885.