Do chromatin changes around a nascent double strand DNA spread spherically into linearly non-adjacent chromatin?

Frontiers in Genetics

Volumn 4, Issue JUL, 2013, Pages

  Savic, Velibor ^a,b  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84883508326     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2013.00139     Document Type: Short Survey

References (42)

1. Bakkenist, C. J., and Kastan, M. B. (2003). DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421, 499-506. doi: 10.1038/nature01368
2. Berkovich, E., Monnat, R. J. Jr., and Kastan, M. B. (2007). Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nat. Cell Biol. 9, 683-690. doi: 10.1038/ncb1599
3. Bredemeyer, A. L., Helmink, B. A., Innes, C. L., Calderon, B., McGinnis, L. M., Mahowald, G. K., et al. (2008). DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes. Nature 456, 819-823. doi: 10.1038/nature07392
4. 2AX in response to DNA double-strand breaks. J. Biol. Chem. 276, 42462-42467. doi: 10.1074/jbc. C100466200
5. 2AX haploinsufficiency modifies genomic stability and tumor susceptibility. Cell 114, 371-383. doi: 10.1016/S0092-8674(03)00567-1
6. 2AX phosphorylation is dispensable for the initial recognition of DNA breaks. Nat. Cell Biol. 5, 675-679. doi: 10.1038/ncb1004
7. Chapman, J. R., Sossick, A. J., Boulton, S. J., and Jackson, S. P. (2012). BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J. Cell Sci. 125, 3529-3534. doi: 10.1242/jcs.105353
8. Ciccia, A., and Elledge, S. J. (2010). The DNA damage response: making it safe to play with knives. Mol. Cell 40, 179-204. doi: 10.1016/j.molcel.2010.09.019
9. Dion, V., and Gasser, S. M. (2013). Chromatin movement in the maintenance of genome stability. Cell 152, 1355-1364. doi: 10.1016/j.cell.2013.02.010
10. Doil, C., Mailand, N., Bekker-Jensen, S., Menard, P., Larsen, D. H., Pepperkok, R., et al. (2009). RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 136, 435-446. doi: 10.1016/j.cell.2008.12.041
11. Gilbert, N., Gilchrist, S., and Bickmore, W. (2005). Chromatin organization in the mammalian nucleus. Int. Rev. Cytol. 242, 283-336. doi: 10.1016/S0074-7696(04) 42007-5
12. Gudjonsson, T., Altmeyer, M., Savic, V., Toledo, L., Dinant, C., Grofte, M., et al. (2012). TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes. Cell 150, 697-709. doi: 10.1016/j.cell.2012.06.039
13. 2AX around DNA double strand breaks in the mammalian genome. EMBO J. 29, 1446-1457. doi: 10.1038/emboj.2010.38
14. 2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break. Mol. Cell 33, 335-343. doi: 10.1016/j.molcel.2009.01.016
15. 2AX modification in yeast and mammals. J. Cell Biol. 178, 209-218. doi: 10.1083/jcb.200612031
16. Kitagawa, R., and Kastan, M. B. (2005). The ATM-dependent DNA damage signaling pathway. Cold Spring Harb. Symp. Quant. Biol. 70, 99-109. doi: 10.1101/sqb.2005.70.002
17. 2AX participates the DNA damage-induced ATM activation through interaction with NBS1. Biochem. Biophys. Res. Commun. 380, 752-775. doi: 10.1016/j.bbrc.2009.01.109
18. Krawczyk, P. M., Borovski, T., Stap, J., Cijsouw, T., ten Cate, R., Medema, J. P., et al. (2012). Chromatin mobility is increased at sites of DNA double-strand breaks. J. Cell Sci. 125, 2127-2133. doi: 10.1242/jcs.089847
19. Kruhlak, M. J., Celeste, A., Dellaire, G., Fernandez-Capetillo, O., Muller, W. G., McNally, J. G., et al. (2006). Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol. 172, 823-834. doi: 10.1083/jcb.200510015
20. Li, J., Coic, E., Lee, K., Lee, C. S., Kim, J. A., Wu, Q., et al. (2012). Regulation of budding yeast mating-type switching donor preference by the FHA domain of Fkh1. PLoS Genet. 8:e1002630. doi: 10.1371/journal.pgen.1002630
21. Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293. doi: 10.1126/science.1181369
22. Lin, C., Yang, L., Tanasa, B., Hutt, K., Ju, B. G., Ohgi, K., et al. (2009). Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139, 1069-1083. doi: 10.1016/j.cell.2009.11.030
23. Lomvardas, S., Barnea, G., Pisapia, D. J., Mendelsohn, M., Kirkland, J., and Axel, R. (2006). Interchromosomal interactions and olfactory receptor choice. Cell 126, 403-413. doi: 10.1016/j.cell.2006.06.035
24. Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R. III, Hurov, K. E., Luo, J., et al. (2007). ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160-1166. doi: 10.1126/science.1140321
25. Meier, A., Fiegler, H., Munoz, P., Ellis, P., Rigler, D., Langford, C., et al. (2007). Spreading of mammalian DNA-damage response factors studied by ChIP-chip at damaged telomeres. EMBO J. 26, 2707-2718. doi: 10.1038/sj.emboj.7601719
26. Panier, S., Ichijima, Y., Fradet-Turcotte, A., Leung, C. C., Kaustov, L., Arrowsmith, C. H., et al. (2012). Tandem protein interaction modules organize the ubiquitindependent response to DNA double-strand breaks. Mol. Cell 47, 383-395. doi: 10.1016/j.molcel.2012.05.045
27. Pankotai, T., Bonhomme, C., Chen, D., and Soutoglou, E. (2012). DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks. Nat. Struct. Mol. Biol. 19, 276-282. doi: 10.1038/nsmb.2224
28. Renkawitz, J., Lademann, C. A., Kalocsay, M., and Jentsch, S. (2013). Monitoring homology search during DNA double-strand break repair in vivo. Mol. Cell 50, 261-272. doi: 10.1016/j.molcel.2013.02.020
29. Rogakou, E. P., Boon, C., Redon, C., and Bonner, W. M. (1999). Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol. 146, 905-916. doi: 10.1083/jcb.146.5.905
30. 2AX phosphorylation on serine 139. J. Biol. Chem. 273, 5858-5868. doi: 10.1074/jbc.273.10.5858
31. 2AX densities in chromatin. Mol. Cell 34, 298-310. doi: 10.1016/j.molcel.2009.04.012
32. Shanbhag, N. M., Rafalska-Metcalf, I. U., Balane-Bolivar, C., Janicki, S. M., and Greenberg, R. A. (2010). ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell 141, 970-981. doi: 10.1016/j.cell.2010.04.038
33. So, S., Davis, A. J., and Chen, D. J. (2009). Autophosphorylation at serine 1981 stabilizes ATM at DNA damage sites. J. Cell Biol. 187, 977-990. doi: 10.1083/jcb.200906064
34. Soutoglou, E., and Misteli, T. (2008). Activation of the cellular DNA damage response in the absence of DNA lesions. Science 320, 1507-1510. doi: 10.1126/science.1159051
35. Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., and Flavell, R. A. (2005). Interchromosomal associations between alternatively expressed loci. Nature 435, 637-645. doi: 10.1038/nature03574
36. Stewart, G. S., Panier, S., Townsend, K., Al-Hakim, A. K., Kolas, N. K., Miller, E. S., et al. (2009). The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 136, 420-434. doi: 10.1016/j.cell.2008.12.042
37. Stewart, G. S., Wang, B., Bignell, C. R., Taylor, A. M., and Elledge, S. J. (2003). MDC1 is a mediator of the mammalian DNA damage checkpoint. Nature 421, 961-966. doi: 10.1038/nature01446
38. Stracker, T. H., and Petrini, J. H. (2011). The MRE11 complex: starting from the ends. Nat. Rev. Mol. Cell Biol. 12, 90-103. doi: 10.1038/nrm3047
39. 2AX and MDC1: anchoring the DNA-damage-response machinery to broken chromosomes. DNA Repair (Amst.) 5, 534-543. doi: 10.1016/j.dnarep.2006.01.012
40. Tsukuda, T., Fleming, A. B., Nickoloff, J. A., and Osley, M. A. (2005). Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 438, 379-383. doi: 10.1038/nature04148
41. You, Z., Bailis, J. M., Johnson, S. A., Dilworth, S. M., and Hunter, T. (2007). Rapid activation of ATM on DNA flanking double-strand breaks. Nat. Cell Biol. 9, 1311-1318. doi: 10.1038/ncb1651
42. Zhang, Y., McCord, R. P., Ho, Y. J., Lajoie, B. R., Hildebrand, D. G., Simon, A. C., et al. (2012). Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908-921. doi: 10.1016/j.cell.2012.02.002