Abstract
Recent advances have led to several systems to study transcription from defined loci in living cells. It has now become possible to address long-standing questions regarding the interplay between the processes of DNA damage repair and transcription—two disparate processes that can occur on the same stretch of chromatin and which both lead to extensive chromatin change. Here we describe the development of a system to create enzymatically induced DNA double-strand breaks (DSBs) at a site of inducible transcription and methods to study the interplay between these processes.
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References
Lukas C, Falck J, Bartkova J, Bartek J, Lukas J (2003) Distinct spatiotemporal dynamics of mammalian checkpoint regulators induced by DNA damage. Nat Cell Biol 5(3):255–260
Bekker-Jensen S, Lukas C, Kitagawa R, Melander F, Kastan MB, Bartek J et al (2006) Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks. J Cell Biol 173(2):195
Lisby M, Barlow JH, Burgess RC, Rothstein R (2004) Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118(6):699–713
Lisby M, Mortensen UH, Rothstein R (2003) Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat Cell Biol 5(6):572–577
Berkovich E, Monnat RJ, Kastan MB (2007) Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nat Cell Biol 9(6):683–690
Pankotai T, Bonhomme C, Chen D, Soutoglou E (2012) DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks. Nat Struct Mol Biol 19(3):276–282
Iacovoni JS, Caron P, Lassadi I, Nicolas E, Massip L, Trouche D et al (2010) High-Âresolution profiling of |[gamma]|H2AX around DNA double strand breaks in the mammalian genome. EMBO J 29(8):1446–1457
Soutoglou E, Dorn JF, Sengupta K, Jasin M, Nussenzweig A, Ried T et al (2007) Positional stability of single double-strand breaks in mammalian cells. Nat Cell Biol 9(6):675–682
Honma M, Izumi M, Sakuraba M, Tadokoro S, Sakamoto H, Wang W et al (2003) Deletion, rearrangement, and gene conversion; genetic consequences of chromosomal double-strand breaks in human cells. Environ Mol Mutagen 42(4):288–298
Rouet P, Smih F, Jasin M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14(12):8096–8106
Anindya R, Ayg\ün O, Svejstrup JQ (2007) Damage-induced ubiquitylation of human RNA polymerase II by the ubiquitin ligase Nedd4, but not Cockayne syndrome proteins or BRCA1. Mol Cell 28(3):386–397
Svejstrup JQ (2007) Contending with transcriptional arrest during RNAPII transcript elongation. Trends Biochem Sci 32(4):165–171
Solovjeva LV, Svetlova MP, Chagin VO, Tomilin NV (2007) Inhibition of transcription at radiation-induced nuclear foci of phosphorylated histone H2AX in mammalian cells. Chromosome Res 15(6):787–797
Kruhlak M, Crouch EE, Orlov M, Montano C, Gorski SA, Nussenzweig A et al (2007) The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature 447(7145):730–734
Shanbhag NM, Rafalska-Metcalf IU, Balane-ÂBolivar C, Janicki SM, Greenberg RA (2010) ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell 141(6):970–981
Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV et al (2004) From silencing to gene expression: real-time analysis in single cells. Cell 116(5):683–698
Rafalska-Metcalf IU, Janicki SM (2007) Show and tell: visualizing gene expression in living cells. J Cell Sci 120(14):2301–2308
Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2(4):437–445
Yunger S, Shav-Tal Y (2011) Imaging mRNAs in living mammalian cells. Methods Mol Biol 714:249–263
Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95(18):10570–10575
Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK (1998) Structure of foki has implications for DNA cleavage. Proc Natl Acad Sci USA 95(18):10564–10569
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Shanbhag, N.M., Greenberg, R.A. (2013). The Dynamics of DNA Damage Repair and Transcription. In: Shav-Tal, Y. (eds) Imaging Gene Expression. Methods in Molecular Biology, vol 1042. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-526-2_16
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DOI: https://doi.org/10.1007/978-1-62703-526-2_16
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Publisher Name: Humana Press, Totowa, NJ
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