Submitted:
23 November 2023
Posted:
24 November 2023
You are already at the latest version
Abstract
Keywords:
1. Introduction
2. Materials and Methods
2.1. Cell culture and treatments
2.2. Synchronization of cells and treatment with etoposide
2.3. Cell lysates and chromatin isolation
2.4. Immunoprecipitation and immunoblotting
2.5. Flow cytometry
2.6. Immunofluorescence Microscopy
3. RESULTS:
3.1. RPA phosphorylation affects ATR signaling in G2 synchronized cells.
3.2. Initial Chk1 phosphorylation during DNA damage in G2 occurs independently of RPA phosphorylation
3.3. RPA phosphorylation promotes chromatin retention and accumulation of TopBP1 and Rad9 in G2
3.4. RPA32 Ser33 phosphorylation indirectly requires ATM activity
3.5. RPA32 Ser4/Ser8 phosphorylation is required for KAP-1 phosphorylation
3.6. RPA32 phosphorylation influences phosphorylation of H2AX and Rad51 chromatin loading
4. Discussion:
5. Abbreviations
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Iliakis, G.; Wang, Y.; Guan, J.; Wang, H. DNA damage checkpoint control in cells exposed to ionizing radiation. Oncogene 2003, 22, 5834–5847. [Google Scholar] [CrossRef] [PubMed]
- Ciccia, A.; Elledge, S.J. The DNA damage response: making it safe to play with knives. Mol Cell 2010, 40, 179–204. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Shibata, A.; Conrad, S.; Birraux, J.; Geuting, V.; Barton, O.; Ismail, A.; Kakarougkas, A.; Meek, K.; Taucher-Scholz, G.; Lobrich, M.; et al. Factors determining DNA double-strand break repair pathway choice in G2 phase. EMBO J 2011, 30, 1079–1092. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Huertas, P. DNA resection in eukaryotes: deciding how to fix the break. Nat Struct Mol Biol PMCID: PMC2850169. 2010, 17, 11–16. [Google Scholar] [CrossRef] [PubMed]
- Symington, L.S.; Gautier, J. Double-strand break end resection and repair pathway choice. Annu Rev Genet 2011, 45, 247–271. [Google Scholar] [CrossRef] [PubMed]
- Shiotani, B.; Zou, L. Single-stranded DNA orchestrates an ATM-to-ATR switch at DNA breaks. Mol Cell 2009, 33, 547–558. [Google Scholar] [CrossRef] [PubMed Central]
- Zou, L.; Elledge, S.J. Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science 2003, 300, 1542–1548. [Google Scholar] [CrossRef] [PubMed]
- Lee, J.; Kumagai, A.; Dunphy, W.G. The Rad9-Hus1-Rad1 checkpoint clamp regulates interaction of TopBP1 with ATR. J Biol Chem 2007, 282, 28036–28044. [Google Scholar] [CrossRef] [PubMed]
- Lee, J.; Dunphy, W.G. Rad17 plays a central role in establishment of the interaction between TopBP1 and the Rad9-Hus1-Rad1 complex at stalled replication forks. Mol Biol Cell 2010, 21, 926–935. [Google Scholar] [CrossRef]
- Chen, R.; Wold, M.S. Replication protein A: single-stranded DNA's first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays 2014, 36, 1156–1161. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Oakley, G.G.; Patrick, S.M. Replication protein A: directing traffic at the intersection of replication and repair. Front Biosci 2010, 15, 883–900. [Google Scholar] [CrossRef]
- Zernik-Kobak, M.; Vasunia, K.; Connelly, M.; Anderson, C.W.; Dixon, K. Sites of UV-induced phosphorylation of the p34 subunit of replication protein A from HeLa cells. J.Biol.Chem. 1997, 272, 23896–23904. [Google Scholar] [CrossRef] [PubMed]
- Niu, H.; Erdjument-Bromage, H.; Pan, Z.Q.; Lee, S.H.; Tempst, P.; Hurwitz, J. Mapping of amino acid residues in the p34 subunit of human single- stranded DNA-binding protein phosphorylated by DNA- dependent protein kinase and Cdc2 kinase in vitro. J.Biol.Chem. 1997, 272, 12634–12641. [Google Scholar] [CrossRef]
- Liu, S.; Opiyo, S.O.; Manthey, K.; Glanzer, J.G.; Ashley, A.K.; Amerin, C.; Troksa, K.; Shrivastav, M.; Nickoloff, J.A.; Oakley, G.G. Distinct roles for DNA-PK, ATM and ATR in RPA phosphorylation and checkpoint activation in response to replication stress. Nucleic Acids Res 2012, 14, 10780–10794. [Google Scholar] [CrossRef] [PubMed]
- Vassin, V.M.; Wold, M.S.; Borowiec, J.A. Replication Protein A (RPA) Phosphorylation Prevents RPA Association with Replication Centers. Mol.Cell Biol 2004, 24, 1930–1943. [Google Scholar] [CrossRef]
- Marechal, A.; Zou, L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res PMCID: PMC4650586. 2015, 25, 9–23. [Google Scholar] [CrossRef] [PubMed]
- Anantha, R.W.; Vassin, V.M.; Borowiec, J.A. Sequential and synergistic modification of human RPA stimulates chromosomal DNA repair. J Biol Chem 2007, 282, 35910–35923. [Google Scholar] [CrossRef]
- Vassin, V.M.; Anantha, R.W.; Sokolova, E.; Kanner, S.; Borowiec, J.A. Human RPA phosphorylation by ATR stimulates DNA synthesis and prevents ssDNA accumulation during DNA-replication stress. J Cell Sci 2009, 122, 4070–4080. [Google Scholar] [CrossRef] [PubMed]
- Shiotani, B.; Nguyen, H.D.; Hakansson, P.; Marechal, A.; Tse, A.; Tahara, H.; Zou, L. Two Distinct Modes of ATR Activation Orchestrated by Rad17 and Nbs1. Cell Rep 2013, 3, 1651–1662. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Oakley, G.G.; Tillison, K.; Opiyo, S.A.; Glanzer, J.G.; Horn, J.M.; Patrick, S.M. Physical interaction between replication protein A (RPA) and MRN: involvement of RPA2 phosphorylation and the N-terminus of RPA1. Biochemistry 2009, 48, 7473–7481. [Google Scholar] [CrossRef] [PubMed]
- Sartori, A.A.; Lukas, C.; Coates, J.; Mistrik, M.; Fu, S.; Bartek, J.; Baer, R.; Lukas, J.; Jackson, S.P. Human CtIP promotes DNA end resection. Nature 2007, 450, 509–514. [Google Scholar] [CrossRef] [PubMed]
- Yamane, A.; Robbiani, D.F.; Resch, W.; Bothmer, A.; Nakahashi, H.; Oliveira, T.; Rommel, P.C.; Brown, E.J.; Nussenzweig, A.; Nussenzweig, M.C. RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle. Cell Rep 2013, 3, 138–147. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Ziv, Y.; Bar-Shira, A.; Pecker, I.; Russell, P.; Jorgensen, T.J.; Tsarfati, I.; Shiloh, Y. Recombinant ATM protein complements the cellular A-T phenotype. Oncogene 1997, 15, 159–167. [Google Scholar] [CrossRef] [PubMed]
- Ziv, Y.; Jaspers, N.G.; Etkin, S.; Danieli, T.; Trakhtenbrot, L.; Amiel, A.; Ravia, Y.; Shiloh, Y. Cellular and molecular characteristics of an immortalized ataxia- telangiectasia (group AB) cell line. Cancer Res. 1989, 49, 2495–2501. [Google Scholar] [PubMed]
- Guo, Z.; Kumagai, A.; Wang, S.X.; Dunphy, W.G. Requirement for Atr in phosphorylation of Chk1 and cell cycle regulation in response to DNA replication blocks and UV-damaged DNA in Xenopus egg extracts. Genes Dev 2000, 14, 2745–2756. [Google Scholar] [CrossRef] [PubMed]
- Zhao, H.; Piwnica-Worms, H. ATR-mediated checkpoint pathways regulate phosphorylation and activation of human Chk1. Mol Cell Biol 2001, 21, 4129–4139. [Google Scholar] [CrossRef] [PubMed]
- Olson, E.; Nievera, C.J.; Klimovich, V.; Fanning, E.; Wu, X. RPA2 is a direct downstream target for ATR to regulate the S-phase checkpoint. J Biol Chem 2006, 281, 39517–39533. [Google Scholar] [CrossRef]
- Liu, Q.; Guntuku, S.; Cui, X.S.; Matsuoka, S.; Cortez, D.; Tamai, K.; Luo, G.; Carattini-Rivera, S.; DeMayo, F.; Bradley, A.; et al. Chk1 is an essential kinase that is regulated by Atr and required for the G(2)/M DNA damage checkpoint. Genes Dev. 2000, 14, 1448–1459. [Google Scholar] [CrossRef]
- Lindsey-Boltz, L.A.; Reardon, J.T.; Wold, M.S.; Sancar, A. In vitro analysis of the role of replication protein A (RPA) and RPA phosphorylation in ATR-mediated checkpoint signaling. J Biol Chem 2012, 287, 36123–36131. [Google Scholar] [CrossRef] [PubMed Central]
- Liaw, H.; Lee, D.; Myung, K. DNA-PK-dependent RPA2 hyperphosphorylation facilitates DNA repair and suppresses sister chromatid exchange. PLoS One 2011, 6, e21424. [Google Scholar] [CrossRef] [PubMed Central]
- Anantha, R.W.; Sokolova, E.; Borowiec, J.A. RPA phosphorylation facilitates mitotic exit in response to mitotic DNA damage. Proc Natl Acad Sci U S A 2008, 105, 12903–12908. [Google Scholar] [CrossRef] [PubMed]
- Carty, M.P.; Zernik-Kobak, M.; McGrath, S.; Dixon, K. UV light-induced DNA synthesis arrest in HeLa cells is associated with changes in phosphorylation of human single- stranded DNA-binding protein. EMBO J. 1994, 13, 2114–2123. [Google Scholar] [CrossRef] [PubMed]
- Stiff, T.; Cerosaletti, K.; Concannon, P.; O'Driscoll, M.; Jeggo, P.A. Replication independent ATR signalling leads to G2/M arrest requiring Nbs1, 53BP1 and MDC1. Hum Mol Genet 2008, 17, 3247–3253. [Google Scholar] [CrossRef]
- Cuadrado, M.; Martinez-Pastor, B.; Murga, M.; Toledo, L.I.; Gutierrez-Martinez, P.; Lopez, E.; Fernandez-Capetillo, O. ATM regulates ATR chromatin loading in response to DNA double-strand breaks. J Exp Med 2006, 203, 297–303. [Google Scholar] [CrossRef] [PubMed]
- Jazayeri, A.; Falck, J.; Lukas, C.; Bartek, J.; Smith, G.C.; Lukas, J.; Jackson, S.P. ATM- and cell cycle-dependent regulation of ATR in response to DNA double-strand breaks. Nat Cell Biol 2006, 8, 37–45. [Google Scholar] [CrossRef]
- Myers, J.S.; Cortez, D. Rapid activation of ATR by ionizing radiation requires ATM and Mre11. J Biol Chem 2006, 281, 9346–9350. [Google Scholar] [CrossRef]
- San Filippo, J.; Sung, P.; Klein, H. Mechanism of eukaryotic homologous recombination. Annu Rev Biochem 2008, 77, 229–257. [Google Scholar] [CrossRef]
- Beucher, A.; Birraux, J.; Tchouandong, L.; Barton, O.; Shibata, A.; Conrad, S.; Goodarzi, A.A.; Krempler, A.; Jeggo, P.A.; Lobrich, M. ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2. EMBO J 2009, 28, 3413–3427. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Soniat, M.M.; Myler, L.R.; Paull, T.T.; Finkelstein, I.J. RPA phosphorylation regulates DNA resection. BioRxiv 2019, 17, 517771. [Google Scholar]
- Lee, D.H.; Pan, Y.; Kanner, S.; Sung, P.; Borowiec, J.A.; Chowdhury, D. A PP4 phosphatase complex dephosphorylates RPA2 to facilitate DNA repair via homologous recombination. Nat Struct Mol Biol 2010, 17, 365–372. [Google Scholar] [CrossRef] [PubMed Central]
- Goodarzi, A.A.; Noon, A.T.; Deckbar, D.; Ziv, Y.; Shiloh, Y.; Lobrich, M.; Jeggo, P.A. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 2008, 31, 167–177. [Google Scholar] [CrossRef] [PubMed]
- Noon, A.T.; Shibata, A.; Rief, N.; Lobrich, M.; Stewart, G.S.; Jeggo, P.A.; Goodarzi, A.A. 53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair. Nat Cell Biol 2010, 12, 177–184. [Google Scholar] [CrossRef] [PubMed]
- Ziv, Y.; Bielopolski, D.; Galanty, Y.; Lukas, C.; Taya, Y.; Schultz, D.C.; Lukas, J.; Bekker-Jensen, S.; Bartek, J.; Shiloh, Y. 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, 870–876. [Google Scholar] [CrossRef] [PubMed]
- Marechal, A.; Zou, L. DNA damage sensing by the ATM and ATR kinases. Cold Spring Harb Perspect Biol 2013, 5. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Elia, A.E.; Wang, D.C.; Willis, N.A.; Boardman, A.P.; Hajdu, I.; Adeyemi, R.O.; Lowry, E.; Gygi, S.P.; Scully, R.; Elledge, S.J. RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Mol Cell 2015, 60, 280–293. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
- Marechal, A.; Li, J.M.; Ji, X.Y.; Wu, C.S.; Yazinski, S.A.; Nguyen, H.D.; Liu, S.; Jimenez, A.E.; Jin, J.; Zou, L. PRP19 transforms into a sensor of RPA-ssDNA after DNA damage and drives ATR activation via a ubiquitin-mediated circuitry. Mol Cell 2014, 53, 235–246. [Google Scholar] [CrossRef] [PubMed Central]
- Ashley, A.K.; Shrivastav, M.; Nie, J.; Amerin, C.; Troksa, K.; Glanzer, J.G.; Liu, S.; Opiyo, S.O.; Dimitrova, D.D.; Le, P.; et al. DNA-PK phosphorylation of RPA32 Ser4/Ser8 regulates replication stress checkpoint activation, fork restart, homologous recombination and mitotic catastrophe. DNA Repair (Amst) 2014, 21, 131–139. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]





Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).