DNA break mapping reveals topoisomerase II activity genome-wide

International Journal of Molecular Sciences

Volumn 15, Issue 7, 2014, Pages 13111-13122

  Baranello, Laura ^a   Kouzine, Fedor ^a   Wojtowicz, Damian ^b   Cui, Kairong ^c   Przytycka, Teresa M ^b   Zhao, Keji ^c   Levens, David ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

DNA damage; Topoisomerases; Transcription

Indexed keywords

DNA NUCLEOTIDYLEXOTRANSFERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); ETOPOSIDE; GENOMIC DNA; DNA;

ARTICLE; CONTROLLED STUDY; DNA NICK TRANSLATION; DNA PURIFICATION; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVITY; GENE EXPRESSION; GENE SEQUENCE; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MOLECULAR WEIGHT; SINGLE STRANDED DNA BREAK; SPECTROPHOTOMETRY; CHROMOSOME MAP; DNA SEQUENCE; HCT116 CELL LINE; METABOLISM;

CHROMOSOME MAPPING; DNA; DNA BREAKS, DOUBLE-STRANDED; DNA BREAKS, SINGLE-STRANDED; DNA TOPOISOMERASES, TYPE II; HCT116 CELLS; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 84905020953     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms150713111     Document Type: Article

References (30)

1. Lindahl, T.; Barnes, D.E. Repair of endogenous DNA damage. Cold Spring Harb. Symp. Quant. Biol. 2000, 65, 127-133.
2. Aguilera, A.; Garcia-Muse, T. Causes of genome instability. Annu. Rev. Genet. 2013, 47, 1-32.
3. Bennett, C.B.; Lewis, A.L.; Baldwin, K.K.; Resnick, M.A. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc. Natl. Acad. Sci. USA 1993, 90, 5613-5617.
4. Sandell, L.L.; Zakian, V.A. Loss of a yeast telomere: Arrest, recovery, and chromosome loss. Cell 1993, 75, 729-739.
5. Jackson, S.P.; Bartek, J. The DNA-damage response in human biology and disease. Nature 2009, 461, 1071-1078.
6. Caldecott, K.W. Mammalian single-strand break repair: Mechanisms and links with chromatin. DNA Repair 2007, 6, 443-453.
7. Ju, B.G.; Lunyak, V.V.; Perissi, V.; Garcia-Bassets, I.; Rose, D.W.; Glass, C.K.; Rosenfeld, M.G. A Topoisomerase IIβ-mediated dsDNA break required for regulated transcription. Science 2006, 312, 1798-1802.
8. Perillo, B.; Ombra, M.N.; Bertoni, A.; Cuozzo, C.; Sacchetti, S.; Sasso, A.; Chiariotti, L.; Malorni, A.; Abbondanza, C.; Avvedimento, E.V. DNA oxidation as triggered by H3K9me2 demethylation drives estrogen-induced gene expression. Science 2008, 319, 202-206.
9. Iacovoni, J.S.; Caron, P.; Lassadi, I.; Nicolas, E.; Massip, L.; Trouche, D.; Legube, G. High-resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome. EMBO J. 2010, 29, 1446-1457.
10. Blitzblau, H.G.; Hochwagen, A. Genome-wide detection of meiotic DNA double-strand break hotspots using single-stranded DNA. Methods Mol. Biol. 2011, 745, 47-63.
11. Crosetto, N.; Mitra, A.; Silva, M.J.; Bienko, M.; Dojer, N.; Wang, Q.; Karaca, E.; Chiarle, R.; Skrzypczak, M.; Ginalski, K., et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 2013, 10, 361-365.
12. Pommier, Y. Drugging topoisomerases: Lessons and challenges. ACS Chem. Biol. 2013, 8, 82-95.
13. Nitiss, J.L. Targeting DNA Topoisomerase II in cancer chemotherapy. Nat. Rev. Cancer 2009, 9, 338-350.
14. Baranello, L.; Kouzine, F.; Levens, D. DNA topoisomerases: Beyond the standard role. Transcription 2013, 4, 232-237.
15. Baldwin, E.L.; Osheroff, N. Etoposide, Topoisomerase II and cancer. Curr. Med. Chem. Anticancer Agents 2005, 5, 363-372.
16. Muslimovic, A.; Nyström, S.; Gao, Y.; Hammarsten, O. Numerical analysis of etoposide induced DNA breaks. PLoS One 2009, 4, e5859.
17. Caldecott, K.W. Single-strand break repair and genetic disease. Nat. Rev. Genet. 2008, 9, 619-631.
18. Nitiss, J.L. DNA Topoisomerase II and its growing repertoire of biological functions. Nat. Rev. Cancer 2009, 9, 327-337.
19. Liu, L.F.; Wang, J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 1987, 84, 7024-7027.
20. Miao, Z.H.; Player, A.; Shankavaram, U.; Wang, Y.H.; Zimonjic, D.B.; Lorenzi, P.L.; Liao, Z.Y.; Liu, H.; Shimura, T.; Zhang, H.L., et al. Nonclassic functions of human Topoisomerase I: Genome-wide and pharmacologic analyses. Cancer Res. 2007, 67, 8752-8761.
21. Kouzine, F.; Gupta, A.; Baranello, L.; Wojtowicz, D.; Ben-Aissa, K.; Liu, J.; Przytycka, T.M.; Levens, D. Transcription-dependent dynamic supercoiling is a short-range genomic force. Nat. Struct. Mol. Biol. 2013, 20, 396-403.
22. Roca, J.; Wang, J.C. The probabilities of supercoil removal and decatenation by yeast DNA Topoisomerase II. Genes Cells 1996, 1, 17-27.
23. Lavelle, C. Forces and torques in the nucleus: Chromatin under mechanical constraints. Biochem. Cell Biol. 2009, 87, 307-322.
24. Kouzine, F.; Wojtowicz, D.; Yamane, A.; Resch, W.; Kieffer-Kwon, K.R.; Bandle, R.; Nelson, S.; Nakahashi, H.; Awasthi, P.; Feigenbaum, L., et al. Global regulation of promoter melting in naïve lymphocytes. Cell 2013, 153, 988-999.
25. Hubbard, T.J.P.; Aken, B.L.; Ayling, S.; Ballester, B.; Beal, K.; Bragin, E.; Brent, S.; Chen, Y.; Clapham, P.; Clarke, L., et al. Ensembl 2009. Nucleic Acids Res. 2009, 37, D690-D697.
26. Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357-359.
27. Shen, L.; Shao, N.; Liu, X.; Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 2014, doi:10.1186/1471-2164-15-284.
28. Cornarotti, M.; Tinelli, S.; Willmore, E.; Zunino, F.; Fisher, L.M.; Austin, C.A.; Capranico, G. Drug sensitivity and sequence specificity of human recombinant DNA topoisomerases IIα (p170) and IIβ (p180). Mol. Pharmacol. 1996, 50, 1463-1471.
29. Willmore, E.; Errington, F.; Tilby, M.J.; Austin, C.A. Formation and longevity of idarubicin-induced DNA Topoisomerase II cleavable complexes in K562 human leukaemia cells. Biochem. Pharmacol. 2002, 63, 1807-1815.
30. Willmore, E.; Frank, A.J.; Padget, K.; Tilby, M.J.; Austin, C.A. Etoposide targets topoisomerase IIα and IIβ in leukemic cells: Isoform-specific cleavable complexes visualized and quantified in situ by a novel immunofluorescence technique. Mol. Pharmacol. 1998, 54, 78-85.