The kinetics of uracil-N-glycosylase distribution inside replication foci

. 2025 Jan 24 ; 15 (1) : 3026. [epub] 20250124

Jazyk angličtina Země Anglie, Velká Británie Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid39849039

Grantová podpora
NU22-08-00148 Ministerstvo Zdravotnictví Ceské Republiky
TN01000013 Technologická Agentura České Republiky
EXCELES, grant number LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy

Odkazy

PubMed 39849039
PubMed Central PMC11757751
DOI 10.1038/s41598-024-84408-x
PII: 10.1038/s41598-024-84408-x
Knihovny.cz E-zdroje

Mismatched nucleobase uracil is commonly repaired through the base excision repair initiated by DNA uracil glycosylases. The data presented in this study strongly indicate that the nuclear uracil-N-glycosylase activity and nuclear protein content in human cell lines is highest in the S phase of the cell cycle and that its distribution kinetics partially reflect the DNA replication activity in replication foci. In this respect, the data demonstrate structural changes of the replication focus related to the uracil-N-glycosylase distribution several dozens of minutes before end of its replication. The analysis also showed that very popular synchronisation protocols based on the double thymidine block can result in changes in the UNG2 content and uracil excision rate. In response, we propose a new method for the description of the changes of the content and the activity of different cell components during cell cycle without the necessity to use synchronisation protocols.

Zobrazit více v PubMed

Pan, M. R., Li, K., Lin, S. Y. & Hung, W. C. Connecting the dots: From DNA damage and repair to aging. Int. J. Mol. Sci.17, 685. 10.3390/ijms17050685 (2016). PubMed PMC

Mjelle, R. et al. Cell cycle regulation of human DNA repair and chromatin remodeling genes. DNA Repair (Amst)30, 53–67. 10.1016/j.dnarep.2015.03.007 (2015). PubMed

Krokan, H. E. & Bjoras, M. Base excision repair. Cold Spring Harb. Perspect. Biol.5, a012583. 10.1101/cshperspect.a012583 (2013). PubMed PMC

Ligasova, A., Rosenberg, I., Bockova, M., Homola, J. & Koberna, K. Anchored linear oligonucleotides: The effective tool for the real-time measurement of uracil DNA glycosylase activity. Open Biol.11, 210136. 10.1098/rsob.210136 (2021). PubMed PMC

Kavli, B. et al. hUNG2 is the major repair enzyme for removal of uracil from U: A matches, U: G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup. J. Biol. Chem.277, 39926–39936. 10.1074/jbc.M207107200 (2002). PubMed

Hardeland, U., Kunz, C., Focke, F., Szadkowski, M. & Schar, P. Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2. Nucleic Acids Res.35, 3859–3867. 10.1093/nar/gkm337 (2007). PubMed PMC

Visnes, T., Akbari, M., Hagen, L., Slupphaug, G. & Krokan, H. E. The rate of base excision repair of uracil is controlled by the initiating glycosylase. DNA Repair (Amst.)7, 1869–1881. 10.1016/j.dnarep.2008.07.012 (2008). PubMed

Hardeland, U. et al. Thymine DNA glycosylase. Prog. Nucleic Acid Res. Mol. Biol.68, 235–253. 10.1016/s0079-6603(01)68103-0 (2001). PubMed

Hagen, L. et al. Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J.27, 51–61. 10.1038/sj.emboj.7601958 (2008). PubMed PMC

Haug, T. et al. Regulation of expression of nuclear and mitochondrial forms of human uracil-DNA glycosylase. Nucleic Acids Res.26, 1449–1457. 10.1093/nar/26.6.1449 (1998). PubMed PMC

Fischer, J. A. & Caradonna, S. J. Analysis of nuclear uracil DNA-glycosylase (nUDG) turnover during the cell cycle. Methods Mol. Biol.1524, 177–188. 10.1007/978-1-4939-6603-5_11 (2017). PubMed

Fischer, J. A., Muller-Weeks, S. & Caradonna, S. Proteolytic degradation of the nuclear isoform of uracil-DNA glycosylase occurs during the S phase of the cell cycle. DNA Repair (Amst)3, 505–513. 10.1016/j.dnarep.2004.01.012 (2004). PubMed

Otterlei, M. et al. Post-replicative base excision repair in replication foci. EMBO J.18, 3834–3844. 10.1093/emboj/18.13.3834 (1999). PubMed PMC

Koberna, K. et al. Electron microscopy of DNA replication in 3-D: Evidence for similar-sized replication foci throughout S-phase. J. Cell Biochem.94, 126–138. 10.1002/jcb.20300 (2005). PubMed

Ligasova, A. & Koberna, K. The organisation of replisomes. DNA Replication—Current Advances, 253–268, Book_10.5772/791 (2011).

Ligasova, A., Raska, I. & Koberna, K. Organization of human replicon: Singles or zipping couples?. J. Struct. Biol.165, 204–213. 10.1016/j.jsb.2008.11.004 (2009). PubMed PMC

Sarno, A. et al. Uracil-DNA glycosylase UNG1 isoform variant supports class switch recombination and repairs nuclear genomic uracil. Nucleic Acids Res.47, 4569–4585. 10.1093/nar/gkz145 (2019). PubMed PMC

Hayran, A. B. et al. RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork. Nucleic Acids Res.52, 784–800. 10.1093/nar/gkad1115 (2024). PubMed PMC

Micozzi, D. et al. Human cytidine deaminase: A biochemical characterization of its naturally occurring variants. Int. J. Biol. Macromol.63, 64–74. 10.1016/j.ijbiomac.2013.10.029 (2014). PubMed PMC

Vassilev, L. T. Cell cycle synchronization at the G2/M phase border by reversible inhibition of CDK1. Cell Cycle5, 2555–2556. 10.4161/cc.5.22.3463 (2006). PubMed

Vassilev, L. T. et al. Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc. Natl. Acad. Sci. U. S. A.103, 10660–10665. 10.1073/pnas.0600447103 (2006). PubMed PMC

Ligasova, A. & Koberna, K. Strengths and weaknesses of cell synchronization protocols based on inhibition of DNA synthesis. Int. J. Mol. Sci.10.3390/ijms221910759 (2021). PubMed PMC

Sakaue-Sawano, A. et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell132, 487–498. 10.1016/j.cell.2007.12.033 (2008). PubMed

Kaida, A. & Miura, M. Differential dependence on oxygen tension during the maturation process between monomeric Kusabira Orange 2 and monomeric Azami Green expressed in HeLa cells. Biochem. Biophys. Res. Commun.421, 855–859. 10.1016/j.bbrc.2012.04.102 (2012). PubMed

McGarry, T. J. & Kirschner, M. W. Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell93, 1043–1053. 10.1016/S0092-8674(00)81209-X (1998). PubMed

Nishitani, H., Lygerou, Z. & Nishimoto, T. Proteolysis of DNA replication licensing factor Cdt1 in S-phase is performed independently of Geminin through its N-terminal region. J. Biol. Chem.279, 30807–30816. 10.1074/jbc.M312644200 (2004). PubMed

Yoshida, K. & Inoue, I. Regulation of Geminin and Cdt1 expression by E2F transcription factors. Oncogene23, 3802–3812. 10.1038/sj.onc.1207488 (2004). PubMed

Zielke, N. & Edgar, B. A. FUCCI sensors: Powerful new tools for analysis of cell proliferation. Wiley Interdiscip. Rev. Dev. Biol.4, 469–487. 10.1002/wdev.189 (2015). PubMed PMC

Seluanov, A. et al. Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat. Proc. Natl. Acad. Sci. U. S. A.106, 19352–19357. 10.1073/pnas.0905252106 (2009). PubMed PMC

Petrova, N. V., Velichko, A. K., Razin, S. V. & Kantidze, O. L. Small molecule compounds that induce cellular senescence. Aging Cell15, 999–1017. 10.1111/acel.12518 (2016). PubMed PMC

Gonzalez-Gualda, E., Baker, A. G., Fruk, L. & Munoz-Espin, D. A guide to assessing cellular senescence in vitro and in vivo. FEBS J.288, 56–80. 10.1111/febs.15570 (2021). PubMed

Kudlova, N., De Sanctis, J. B. & Hajduch, M. Cellular senescence: Molecular targets, biomarkers, and senolytic drugs. Int. J. Mol. Sci.10.3390/ijms23084168 (2022). PubMed PMC

Torseth, K. et al. The UNG2 Arg88Cys variant abrogates RPA-mediated recruitment of UNG2 to single-stranded DNA. DNA Repair11, 559–569. 10.1016/j.dnarep.2012.03.006 (2012). PubMed

Zeman, M. K. & Cimprich, K. A. Causes and consequences of replication stress. Nat. Cell Biol.16, 2–9. 10.1038/ncb2897 (2014). PubMed PMC

Darzynkiewicz, Z., Halicka, H. D., Zhao, H. & Podhorecka, M. Cell synchronization by inhibitors of DNA replication induces replication stress and DNA damage response: Analysis by flow cytometry. Methods Mol. Biol.761, 85–96. 10.1007/978-1-61779-182-6_6 (2011). PubMed PMC

Halicka, D. et al. DNA damage response resulting from replication stress induced by synchronization of cells by inhibitors of DNA replication: Analysis by flow cytometry. Methods Mol. Biol.1524, 107–119. 10.1007/978-1-4939-6603-5_7 (2017). PubMed

Kurose, A., Tanaka, T., Huang, X., Traganos, F. & Darzynkiewicz, Z. Synchronization in the cell cycle by inhibitors of DNA replication induces histone H2AX phosphorylation: An indication of DNA damage. Cell Prolif.39, 231–240. 10.1111/j.1365-2184.2006.00380.x (2006). PubMed PMC

Hammond, E. M., Green, S. L. & Giaccia, A. J. Comparison of hypoxia-induced replication arrest with hydroxyurea and aphidicolin-induced arrest. Mutat. Res.532, 205–213. 10.1016/j.mrfmmm.2003.08.017 (2003). PubMed

Gong, J., Traganos, F. & Darzynkiewicz, Z. Growth imbalance and altered expression of cyclins B1, A, E, and D3 in MOLT-4 cells synchronized in the cell cycle by inhibitors of DNA replication. Cell Growth Differ.6, 1485–1493 (1995). PubMed

De Brabander, M. J., Van de Veire, R. M., Aerts, F. E., Borgers, M. & Janssen, P. A. The effects of methyl (5-(2-thienylcarbonyl)-1H-benzimidazol-2-yl) carbamate, (R 17934; NSC 238159), a new synthetic antitumoral drug interfering with microtubules, on mammalian cells cultured in vitro. Cancer Res.36, 905–916 (1976). PubMed

Salmon, E. D., McKeel, M. & Hays, T. Rapid rate of tubulin dissociation from microtubules in the mitotic spindle in vivo measured by blocking polymerization with colchicine. J. Cell Biol.99, 1066–1075. 10.1083/jcb.99.3.1066 (1984). PubMed PMC

Javanmoghadam-Kamrani, S. & Keyomarsi, K. Synchronization of the cell cycle using lovastatin. Cell Cycle7, 2434–2440. 10.4161/cc.6364 (2008). PubMed

Park, S. Y. et al. Mimosine arrests the cell cycle prior to the onset of DNA replication by preventing the binding of human Ctf4/And-1 to chromatin via Hif-1alpha activation in HeLa cells. Cell Cycle11, 761–766. 10.4161/cc.11.4.19209 (2012). PubMed

Zwanenburg, T. S. Standardized shake-off to synchronize cultured CHO cells. Mutat Res.120, 151–159. 10.1016/0165-7992(83)90157-4 (1983). PubMed

Nakamura, H., Morita, T. & Sato, C. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp. Cell Res.165, 291–297. 10.1016/0014-4827(86)90583-5 (1986). PubMed

Manders, E. M., Stap, J., Brakenhoff, G. J., van Driel, R. & Aten, J. A. Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. J. Cell Sci.103(Pt 3), 857–862. 10.1242/jcs.103.3.857 (1992). PubMed

Leonhardt, H. et al. Dynamics of DNA replication factories in living cells. J. Cell Biol.149, 271–280. 10.1083/jcb.149.2.271 (2000). PubMed PMC

Ligasova, A. et al. Dr Jekyll and Mr Hyde: a strange case of 5-ethynyl-2 ’-deoxyuridine and 5-ethynyl-2 ’- deoxycytidine. Open Biol.6, 150172. 10.1098/rsob.150172 (2016). PubMed PMC

Ligasova, A. & Koberna, K. Quantification of fixed adherent cells using a strong enhancer of the fluorescence of DNA dyes. Sci. Rep.9, 8701. 10.1038/s41598-019-45217-9 (2019). PubMed PMC

Ligasova, A., Liboska, R., Rosenberg, I. & Koberna, K. The fingerprint of anti-bromodeoxyuridine antibodies and its use for the assessment of their affinity to 5-bromo-2’-deoxyuridine in cellular DNA under various conditions. PLoS One10, e0132393. 10.1371/journal.pone.0132393 (2015). PubMed PMC

Ligasova, A., Strunin, D., Friedecky, D., Adam, T. & Koberna, K. A fatal combination: A thymidylate synthase inhibitor with DNA damaging activity. PLoS One10, e0117459. 10.1371/journal.pone.0117459 (2015). PubMed PMC

Ligasova, A., Konecny, P., Frydrych, I. & Koberna, K. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2’-deoxyuridine, low concentration of hydrochloric acid and exonuclease III. PLoS One12, e0175880. 10.1371/journal.pone.0175880 (2017). PubMed PMC

Ligasova, A., Konecny, P., Frydrych, I. & Koberna, K. Looking for ugly ducklings: The role of the stability of BrdU-antibody complex and the improved method of the detection of DNA replication. PLoS One12, e0174893. 10.1371/journal.pone.0174893 (2017). PubMed PMC

Cvackova, Z. et al. Pontin is localized in nucleolar fibrillar centers. Chromosoma117, 487–497. 10.1007/s00412-008-0170-8 (2008). PubMed PMC

Ligasova, A. et al. A new sensitive method for the detection of mycoplasmas using fluorescence microscopy. Cells8, 1510. 10.3390/cells8121510 (2019). PubMed PMC

Ligasova, A., Pisklakova, B., Friedecky, D. & Koberna, K. A new technique for the analysis of metabolic pathways of cytidine analogues and cytidine deaminase activities in cells. Sci. Rep.13, 20530. 10.1038/s41598-023-47792-4 (2023). PubMed PMC

Romero-Calvo, I. et al. Reversible Ponceau staining as a loading control alternative to actin in Western blots. Anal. Biochem.401, 318–320. 10.1016/j.ab.2010.02.036 (2010). PubMed

Miller, L. P. ImageJ gel analysis, http://www.lukemiller.org/ImageJ_gel_analysis.pdf (2010).

Ligasova, A. & Koberna, K. New Concept and Apparatus for Cytocentrifugation and Cell Processing for Microscopy Analysis. Int J Mol Sci22, 10.3390/ijms22137098 (2021). PubMed PMC

Berg, S. et al. ilastik: Interactive machine learning for (bio)image analysis. Nat. Methods16, 1226–1232. 10.1038/s41592-019-0582-9 (2019). PubMed

Carpenter, A. E. et al. Cell Profiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol.7, R100. 10.1186/gb-2006-7-10-r100 (2006). PubMed PMC

Kamentsky, L. et al. Improved structure, function and compatibility for cell profiler: Modular high-throughput image analysis software. Bioinformatics27, 1179–1180. 10.1093/bioinformatics/btr095 (2011). PubMed PMC

Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods9, 676–682. 10.1038/nmeth.2019 (2012). PubMed PMC

Van Rossum, G. & Drake, F. L. Python 3 Reference Manual. (Createspace, 2009).

Harris, C. R. et al. Array programming with NumPy. Nature585, 357–362. 10.1038/s41586-020-2649-2 (2020). PubMed PMC

McKinney, W. In Proceedings of the 9th Python in Science Conference 51–56.

Virtanen, P. et al. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat. Methods17, 261–272. 10.1038/s41592-019-0686-2 (2020). PubMed PMC

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

A Rapid Approach for Identifying Cell Lines Lacking Functional Cytidine Deaminase

. 2025 Apr 03 ; 26 (7) : . [epub] 20250403

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...