53BP1-dependent Robust Localized KAP-1 Phosphorylation is Essential for Heterochromatic DNA Double-strand Break Repair

Overview

Journal Nat Cell Biol

Specialty Cell Biology

Date 2010 Jan 19

PMID 20081839

Citations 191

Authors

Angela T Noon

Atsushi Shibata

Nicole Rief

Markus Lobrich

Grant S Stewart

Penelope A Jeggo

Aaron A Goodarzi

Affiliations

Soon will be listed here.

Abstract

DNA double-strand breaks (DSBs) trigger ATM (ataxia telangiectasia mutated) signalling and elicit genomic rearrangements and chromosomal fragmentation if misrepaired or unrepaired. Although most DSB repair is ATM-independent, approximately 15% of ionizing radiation (IR)-induced breaks persist in the absence of ATM-signalling. 53BP1 (p53-binding protein 1) facilitates ATM-dependent DSB repair but is largely dispensable for ATM activation or checkpoint arrest. ATM promotes DSB repair within heterochromatin by phosphorylating KAP-1 (KRAB-associated protein 1, also known as TIF1beta, TRIM28 or KRIP-1; ref. 2). Here, we show that the ATM signalling mediator proteins MDC1, RNF8, RNF168 and 53BP1 are also required for heterochromatic DSB repair. Although KAP-1 phosphorylation is critical for 53BP1-mediated repair, overall phosphorylated KAP-1 (pKAP-1) levels are only modestly affected by 53BP1 loss. pKAP-1 is transiently pan-nuclear but also forms foci overlapping with gammaH2AX in heterochromatin. Cells that do not form 53BP1 foci, including human RIDDLE (radiosensitivity, immunodeficiency, dysmorphic features and learning difficulties) syndrome cells, fail to form pKAP-1 foci. 53BP1 amplifies Mre11-NBS1 accumulation at late-repairing DSBs, concentrating active ATM and leading to robust, localized pKAP-1. We propose that ionizing-radiation induced foci (IRIF) spatially concentrate ATM activity to promote localized alterations in regions of chromatin otherwise inhibitory to repair.

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References

Li X, Lee Y, Jeng J, Yen Y, Schultz D, Shih H . Role for KAP1 serine 824 phosphorylation and sumoylation/desumoylation switch in regulating KAP1-mediated transcriptional repression. J Biol Chem. 2007; 282(50):36177-89. DOI: 10.1074/jbc.M706912200. View

Yu X, Chini C, He M, Mer G, Chen J . The BRCT domain is a phospho-protein binding domain. Science. 2003; 302(5645):639-42. DOI: 10.1126/science.1088753. View

Goodarzi A, Noon A, Deckbar D, Ziv Y, Shiloh Y, Lobrich M . ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell. 2008; 31(2):167-77. DOI: 10.1016/j.molcel.2008.05.017. View

Lee Y, Thomas S, Yang A, Ann D . Doxorubicin down-regulates Kruppel-associated box domain-associated protein 1 sumoylation that relieves its transcription repression on p21WAF1/CIP1 in breast cancer MCF-7 cells. J Biol Chem. 2006; 282(3):1595-606. DOI: 10.1074/jbc.M606306200. View

Mirzoeva O, Petrini J . DNA damage-dependent nuclear dynamics of the Mre11 complex. Mol Cell Biol. 2000; 21(1):281-8. PMC: 88801. DOI: 10.1128/MCB.21.1.281-288.2001. View

Ziv Y, Bielopolski D, Galanty Y, Lukas C, Taya Y, Schultz D . Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat Cell Biol. 2006; 8(8):870-6. DOI: 10.1038/ncb1446. View

Bekker-Jensen S, Lukas C, Kitagawa R, Melander F, Kastan M, Bartek J . Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks. J Cell Biol. 2006; 173(2):195-206. PMC: 2063811. DOI: 10.1083/jcb.200510130. View

Doil C, Mailand N, Bekker-Jensen S, Menard P, Larsen D, Pepperkok R . RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell. 2009; 136(3):435-46. DOI: 10.1016/j.cell.2008.12.041. View

Manke I, Lowery D, Nguyen A, Yaffe M . BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science. 2003; 302(5645):636-9. DOI: 10.1126/science.1088877. View

10.

Riballo E, Kuhne M, Rief N, Doherty A, Smith G, Recio M . A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to gamma-H2AX foci. Mol Cell. 2004; 16(5):715-24. DOI: 10.1016/j.molcel.2004.10.029. View

11.

Stewart G, Panier S, Townsend K, Al-Hakim A, Kolas N, Miller E . The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell. 2009; 136(3):420-34. DOI: 10.1016/j.cell.2008.12.042. View

12.

Lee J, Goodarzi A, Jeggo P, Paull T . 53BP1 promotes ATM activity through direct interactions with the MRN complex. EMBO J. 2009; 29(3):574-85. PMC: 2830698. DOI: 10.1038/emboj.2009.372. View

13.

Iwabuchi K, Basu B, Kysela B, Kurihara T, Shibata M, Guan D . Potential role for 53BP1 in DNA end-joining repair through direct interaction with DNA. J Biol Chem. 2003; 278(38):36487-95. DOI: 10.1074/jbc.M304066200. View

14.

Riballo E, Woodbine L, Stiff T, Walker S, Goodarzi A, Jeggo P . XLF-Cernunnos promotes DNA ligase IV-XRCC4 re-adenylation following ligation. Nucleic Acids Res. 2008; 37(2):482-92. PMC: 2632933. DOI: 10.1093/nar/gkn957. View

15.

Chapman J, Jackson S . Phospho-dependent interactions between NBS1 and MDC1 mediate chromatin retention of the MRN complex at sites of DNA damage. EMBO Rep. 2008; 9(8):795-801. PMC: 2442910. DOI: 10.1038/embor.2008.103. View

16.

Downs J, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N . Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol Cell. 2004; 16(6):979-90. DOI: 10.1016/j.molcel.2004.12.003. View

17.

Derbyshire D, Basu B, Serpell L, Joo W, Date T, Iwabuchi K . Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. EMBO J. 2002; 21(14):3863-72. PMC: 126127. DOI: 10.1093/emboj/cdf383. View

18.

Stucki M, Jackson S . MDC1/NFBD1: a key regulator of the DNA damage response in higher eukaryotes. DNA Repair (Amst). 2004; 3(8-9):953-7. DOI: 10.1016/j.dnarep.2004.03.007. View

19.

Stewart G, Stankovic T, Byrd P, Wechsler T, Miller E, Huissoon A . RIDDLE immunodeficiency syndrome is linked to defects in 53BP1-mediated DNA damage signaling. Proc Natl Acad Sci U S A. 2007; 104(43):16910-5. PMC: 2040433. DOI: 10.1073/pnas.0708408104. View

20.

Lee J, Paull T . Direct activation of the ATM protein kinase by the Mre11/Rad50/Nbs1 complex. Science. 2004; 304(5667):93-6. DOI: 10.1126/science.1091496. View