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NCAPH Stabilizes GEN1 in Chromatin to Resolve Ultra-Fine DNA Bridges and Maintain Chromosome Stability

  • Kim, Jae Hyeong (Department of Internal Medicine, Seoul National University Bundang Hospital) ;
  • Youn, Yuna (Department of Internal Medicine, Seoul National University Bundang Hospital) ;
  • Hwang, Jin-Hyeok (Department of Internal Medicine, Seoul National University Bundang Hospital)
  • Received : 2022.03.25
  • Accepted : 2022.07.17
  • Published : 2022.11.30

Abstract

Repairing damaged DNA and removing all physical connections between sister chromosomes is important to ensure proper chromosomal segregation by contributing to chromosomal stability. Here, we show that the depletion of non-SMC condensin I complex subunit H (NCAPH) exacerbates chromosome segregation errors and cytokinesis failure owing to sister-chromatid intertwinement, which is distinct from the ultra-fine DNA bridges induced by DNA inter-strand crosslinks (DNA-ICLs). Importantly, we identified an interaction between NCAPH and GEN1 in the chromatin involving binding at the N-terminus of NCAPH. DNA-ICL activation, using ICL-inducing agents, increased the expression and interaction between NCAPH and GEN1 in the soluble nuclear and chromatin, indicating that the NCAPH-GEN1 interaction participates in repairing DNA damage. Moreover, NCAPH stabilizes GEN1 within chromatin at the G2/M-phase and is associated with DNA-ICL-induced damage repair. Therefore, NCAPH resolves DNA-ICL-induced ultra-fine DNA bridges by stabilizing GEN1 and ensures proper chromosome separation and chromosome structural stability.

Keywords

Acknowledgement

This work was supported by grant No. NRF-2021R1A2C200708811 from the National Research Foundation of Korea (NRF). We would like to thank Editage (www.editage.co.kr) for English language editing.

References

  1. Bessho, T. (2003). Induction of DNA replication-mediated double strand breaks by psoralen DNA interstrand cross-links. J. Biol. Chem. 278, 5250-5254. https://doi.org/10.1074/jbc.M212323200
  2. Bittmann, J., Grigaitis, R., Galanti, L., Amarell, S., Wilfling, F., Matos, J., and Pfander, B. (2020). An advanced cell cycle tag toolbox reveals principles underlying temporal control of structure-selective nucleases. Elife 9, e52459. https://doi.org/10.7554/eLife.52459
  3. Blanco, M.G., Matos, J., and West, S.C. (2014). Dual control of Yen1 nuclease activity and cellular localization by Cdk and Cdc14 prevents genome instability. Mol. Cell 54, 94-106. https://doi.org/10.1016/j.molcel.2014.02.011
  4. Bredberg, A., Lambert, B., and Soderhall, S. (1982). Induction and repair of psoralen cross-links in DNA of normal human and xeroderma pigmentosum fibroblasts. Mutat. Res. 93, 221-234. https://doi.org/10.1016/0027-5107(82)90137-3
  5. Chan, K.L., Palmai-Pallag, T., Ying, S., and Hickson, I.D. (2009). Replication stress induces sister-chromatid bridging at fragile site loci in mitosis. Nat. Cell Biol. 11, 753-760. https://doi.org/10.1038/ncb1882
  6. Chan, Y.W., Fugger, K., and West, S.C. (2018). Unresolved recombination intermediates lead to ultra-fine anaphase bridges, chromosome breaks and aberrations. Nat. Cell Biol. 20, 92-103. https://doi.org/10.1038/s41556-017-0011-1
  7. Chan, Y.W. and West, S.C. (2014). Spatial control of the GEN1 Holliday junction resolvase ensures genome stability. Nat. Commun. 5, 4844. https://doi.org/10.1038/ncomms5844
  8. Chanboonyasitt, P. and Chan, Y.W. (2021). Regulation of mitotic chromosome architecture and resolution of ultrafine anaphase bridges by PICH. Cell Cycle 20, 2077-2090. https://doi.org/10.1080/15384101.2021.1970877
  9. Chen, E.S., Sutani, T., and Yanagida, M. (2004). Cti1/C1D interacts with condensin SMC hinge and supports the DNA repair function of condensin. Proc. Natl. Acad. Sci. U. S. A. 101, 8078-8083. https://doi.org/10.1073/pnas.0307976101
  10. Chen, G. and Deng, X. (2018). Cell synchronization by double thymidine block. Bio Protoc. 8, e2994.
  11. Chen, X.B., Melchionna, R., Denis, C.M., Gaillard, P.H.L., Blasina, A., Van de Weyer, I., Boddy, M.N., Russell, P., Vialard, J., and McGowan, C.H. (2001). Human Mus81-associated endonuclease cleaves Holliday junctions in vitro. Mol. Cell 8, 1117-1127. https://doi.org/10.1016/S1097-2765(01)00375-6
  12. Ciccia, A., Constantinou, A., and West, S.C. (2003). Identification and characterization of the human mus81-eme1 endonuclease. J. Biol. Chem. 278, 25172-25178. https://doi.org/10.1074/jbc.M302882200
  13. Dardalhon, M. and Averbeck, D. (1995). Pulsed-field gel electrophoresis analysis of the repair of psoralen plus UVA induced DNA photoadducts in Saccharomyces cerevisiae. Mutat. Res. 336, 49-60. https://doi.org/10.1016/0921-8777(94)00037-7
  14. De Silva, I.U., McHugh, P.J., Clingen, P.H., and Hartley, J.A. (2000). Defining the roles of nucleotide excision repair and recombination in the repair of DNA interstrand cross-links in mammalian cells. Mol. Cell. Biol. 20, 7980-7990. https://doi.org/10.1128/MCB.20.21.7980-7990.2000
  15. Deans, A.J. and West, S.C. (2011). DNA interstrand crosslink repair and cancer. Nat. Rev. Cancer 11, 467-480. https://doi.org/10.1038/nrc3088
  16. Dehe, P.M. and Gaillard, P.H.L. (2017). Control of structure-specific endonucleases to maintain genome stability. Nat. Rev. Mol. Cell Biol. 18, 315-330. https://doi.org/10.1038/nrm.2016.177
  17. Dej, K.J., Ahn, C., and Orr-Weaver, T.L. (2004). Mutations in the Drosophila condensin subunit dCAP-G: defining the role of condensin for chromosome condensation in mitosis and gene expression in interphase. Genetics 168, 895-906. https://doi.org/10.1534/genetics.104.030908
  18. Eissler, C.L., Mazon, G., Powers, B.L., Savinov, S.N., Symington, L.S., and Hall, M.C. (2014). The Cdk/cDc14 module controls activation of the Yen1 holliday junction resolvase to promote genome stability. Mol. Cell 54, 80-93. https://doi.org/10.1016/j.molcel.2014.02.012
  19. Elbatsh, A.M.O., Kim, E., Eeftens, J.M., Raaijmakers, J.A., van der Weide, R.H., Garcia-Nieto, A., Bravo, S., Ganji, M., Uit de Bos, J., Teunissen, H., et al. (2019). Distinct roles for condensin's two ATPase sites in chromosome condensation. Mol. Cell 76, 724-737.e5. https://doi.org/10.1016/j.molcel.2019.09.020
  20. Fekairi, S., Scaglione, S., Chahwan, C., Taylor, E.R., Tissier, A., Coulon, S., Dong, M.Q., Ruse, C., Yates, J.R., 3rd, Russell, P., et al. (2009). Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell 138, 78-89. https://doi.org/10.1016/j.cell.2009.06.029
  21. Garcia-Luis, J., Clemente-Blanco, A., Aragon, L., and Machin, F. (2014). Cdc14 targets the Holliday junction resolvase Yen1 to the nucleus in early anaphase. Cell Cycle 13, 1392-1399. https://doi.org/10.4161/cc.28370
  22. Georges, S.A., Biery, M.C., Kim, S.Y., Schelter, J.M., Guo, J., Chang, A.N., Jackson, A.L., Carleton, M.O., Linsley, P.S., Cleary, M.A., et al. (2008). Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215. Cancer Res. 68, 10105-10112. https://doi.org/10.1158/0008-5472.CAN-08-1846
  23. Gibcus, J.H., Samejima, K., Goloborodko, A., Samejima, I., Naumova, N., Nuebler, J., Kanemaki, M.T., Xie, L., Paulson, J.R., Earnshaw, W.C., et al. (2018). A pathway for mitotic chromosome formation. Science 359, eaao6135. https://doi.org/10.1126/science.aao6135
  24. Green, L.C., Kalitsis, P., Chang, T.M., Cipetic, M., Kim, J.H., Marshall, O., Turnbull, L., Whitchurch, C.B., Vagnarelli, P., Samejima, K., et al. (2012). Contrasting roles of condensin I and condensin II in mitotic chromosome formation. J. Cell Sci. 125, 1591-1604.
  25. Grigaitis, R., Ranjha, L., Wild, P., Kasaciunaite, K., Ceppi, I., Kissling, V., Henggeler, A., Susperregui, A., Peter, M., Seidel, R., et al. (2020). Phosphorylation of the RecQ helicase Sgs1/BLM controls its DNA unwinding activity during meiosis and mitosis. Dev. Cell 53, 706-723.e5. https://doi.org/10.1016/j.devcel.2020.05.016
  26. Heale, J.T., Ball, A.R., Jr., Schmiesing, J.A., Kim, J.S., Kong, X., Zhou, S., Hudson, D.F., Earnshaw, W.C., and Yokomori, K. (2006). Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA singlestrand break repair. Mol. Cell 21, 837-848. https://doi.org/10.1016/j.molcel.2006.01.036
  27. Hirano, T. (2012). Condensins: universal organizers of chromosomes with diverse functions. Genes Dev. 26, 1659-1678. https://doi.org/10.1101/gad.194746.112
  28. Hirano, T. (2016). Condensin-based chromosome organization from bacteria to vertebrates. Cell 164, 847-857. https://doi.org/10.1016/j.cell.2016.01.033
  29. Holliday, R. (2007). A mechanism for gene conversion in fungi. Genet. Res. 89, 285-307. https://doi.org/10.1017/S0016672308009476
  30. Hustedt, N. and Durocher, D. (2016). The control of DNA repair by the cell cycle. Nat. Cell Biol. 19, 1-9. https://doi.org/10.1038/ncb3452
  31. Ip, S.C., Rass, U., Blanco, M.G., Flynn, H.R., Skehel, J.M., and West, S.C. (2008). Identification of Holliday junction resolvases from humans and yeast. Nature 456, 357-361. https://doi.org/10.1038/nature07470
  32. Kim, J.H., Youn, Y., Kim, K.T., Jang, G., and Hwang, J.H. (2019). NonSMC condensin I complex subunit H mediates mature chromosome condensation and DNA damage in pancreatic cancer cells. Sci. Rep. 9, 17889. https://doi.org/10.1038/s41598-019-54478-3
  33. Kosugi, S., Hasebe, M., Tomita, M., and Yanagawa, H. (2009). Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc. Natl. Acad. Sci. U. S. A. 106, 10171-10176. https://doi.org/10.1073/pnas.0900604106
  34. Lamothe, R., Costantino, L., and Koshland, D.E. (2020). The spatial regulation of condensin activity in chromosome condensation. Genes Dev. 34, 819-831. https://doi.org/10.1101/gad.335471.119
  35. Lee, H. and Seo, P.J. (2021). HiCORE: Hi-C analysis for identification of core chromatin looping regions with higher resolution. Mol. Cells 44, 883-892. https://doi.org/10.14348/molcells.2021.0014
  36. Lehmann, A.R. (2005). The role of SMC proteins in the responses to DNA damage. DNA Repair (Amst.) 4, 309-314. https://doi.org/10.1016/j.dnarep.2004.07.009
  37. Li, P., Jin, H., and Yu, H.G. (2014). Condensin suppresses recombination and regulates double-strand break processing at the repetitive ribosomal DNA array to ensure proper chromosome segregation during meiosis in budding yeast. Mol. Biol. Cell 25, 2934-2947. https://doi.org/10.1091/mbc.e14-05-0957
  38. Li, X. and Heyer, W.D. (2008). Homologous recombination in DNA repair and DNA damage tolerance. Cell Res. 18, 99-113. https://doi.org/10.1038/cr.2008.1
  39. Lopez-Martinez, D., Liang, C.C., and Cohn, M.A. (2016). Cellular response to DNA interstrand crosslinks: the Fanconi anemia pathway. Cell. Mol. Life Sci. 73, 3097-3114. https://doi.org/10.1007/s00018-016-2218-x
  40. Machin, F. (2020). Implications of metastable nicks and nicked Holliday junctions in processing joint molecules in mitosis and meiosis. Genes (Basel) 11, 1498. https://doi.org/10.3390/genes11121498
  41. Matos, J., Blanco, M.G., Maslen, S., Skehel, J.M., and West, S.C. (2011). Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell 147, 158-172. https://doi.org/10.1016/j.cell.2011.08.032
  42. McHugh, P.J., Sones, W.R., and Hartley, J.A. (2000). Repair of intermediate structures produced at DNA interstrand cross-links in Saccharomyces cerevisiae. Mol. Cell. Biol. 20, 3425-3433. https://doi.org/10.1128/MCB.20.10.3425-3433.2000
  43. Niedernhofer, L.J., Odijk, H., Budzowska, M., van Drunen, E., Maas, A., Theil, A.F., de Wit, J., Jaspers, N.G., Beverloo, H.B., Hoeijmakers, J.H., et al. (2004). The structure-specific endonuclease Ercc1-Xpf is required to resolve DNA interstrand cross-link-induced double-strand breaks. Mol. Cell. Biol. 24, 5776-5787. https://doi.org/10.1128/MCB.24.13.5776-5787.2004
  44. Ono, T., Losada, A., Hirano, M., Myers, M.P., Neuwald, A.F., and Hirano, T. (2003). Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell 115, 109-121. https://doi.org/10.1016/S0092-8674(03)00724-4
  45. Pichierri, P., Averbeck, D., and Rosselli, F. (2002). DNA cross-linkdependent RAD50/MRE11/NBS1 subnuclear assembly requires the Fanconi anemia C protein. Hum. Mol. Genet. 11, 2531-2546. https://doi.org/10.1093/hmg/11.21.2531
  46. Redon, C., Pilch, D., Rogakou, E., Sedelnikova, O., Newrock, K., and Bonner, W. (2002). Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12, 162-169. https://doi.org/10.1016/S0959-437X(02)00282-4
  47. Rothfuss, A. and Grompe, M. (2004). Repair kinetics of genomic interstrand DNA cross-links: evidence for DNA double-strand breakdependent activation of the Fanconi anemia/BRCA pathway. Mol. Cell. Biol. 24, 123-134. https://doi.org/10.1128/MCB.24.1.123-134.2004
  48. Sarbajna, S., Davies, D., and West, S.C. (2014). Roles of SLX1-SLX4, MUS81-EME1, and GEN1 in avoiding genome instability and mitotic catastrophe. Genes Dev. 28, 1124-1136. https://doi.org/10.1101/gad.238303.114
  49. Shintomi, K. and Hirano, T. (2011). The relative ratio of condensin I to II determines chromosome shapes. Genes Dev. 25, 1464-1469. https://doi.org/10.1101/gad.2060311
  50. Thadani, R., Uhlmann, F., and Heeger, S. (2012). Condensin, chromatin crossbarring and chromosome condensation. Curr. Biol. 22, R1012-R1021. https://doi.org/10.1016/j.cub.2012.10.023
  51. Thiriet, C. and Hayes, J.J. (2005). Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. Mol. Cell 18, 617-622. https://doi.org/10.1016/j.molcel.2005.05.008
  52. Walther, N., Hossain, M.J., Politi, A.Z., Koch, B., Kueblbeck, M., OdegardFougner, O., Lampe, M., and Ellenberg, J. (2018). A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. J. Cell Biol. 217, 2309-2328. https://doi.org/10.1083/jcb.201801048
  53. Wang, L.H., Mayer, B., Stemmann, O., and Nigg, E.A. (2010). Centromere DNA decatenation depends on cohesin removal and is required for mammalian cell division. J. Cell Sci. 123, 806-813. https://doi.org/10.1242/jcs.058255
  54. Wang, L.H., Schwarzbraun, T., Speicher, M.R., and Nigg, E.A. (2008). Persistence of DNA threads in human anaphase cells suggests late completion of sister chromatid decatenation. Chromosoma 117, 123-135. https://doi.org/10.1007/s00412-007-0131-7
  55. Wechsler, T., Newman, S., and West, S.C. (2011). Aberrant chromosome morphology in human cells defective for Holliday junction resolution. Nature 471, 642-646. https://doi.org/10.1038/nature09790
  56. Whitfield, M.L., Zheng, L.X., Baldwin, A., Ohta, T., Hurt, M.M., and Marzluff, W.F. (2000). Stem-loop binding protein, the protein that binds the 3' end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms. Mol. Cell. Biol. 20, 4188-4198. https://doi.org/10.1128/MCB.20.12.4188-4198.2000
  57. Wood, J.L., Liang, Y., Li, K., and Chen, J. (2008). Microcephalin/MCPH1 associates with the Condensin II complex to function in homologous recombination repair. J. Biol. Chem. 283, 29586-29592. https://doi.org/10.1074/jbc.M804080200
  58. Wyatt, H.D., Sarbajna, S., Matos, J., and West, S.C. (2013). Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells. Mol. Cell 52, 234-247. https://doi.org/10.1016/j.molcel.2013.08.035
  59. Yu, H.G. and Koshland, D.E. (2003). Meiotic condensin is required for proper chromosome compaction, SC assembly, and resolution of recombination-dependent chromosome linkages. J. Cell Biol. 163, 937-947. https://doi.org/10.1083/jcb.200308027
  60. Zhang, J. and Walter, J.C. (2014). Mechanism and regulation of incisions during DNA interstrand cross-link repair. DNA Repair (Amst.) 19, 135-142. https://doi.org/10.1016/j.dnarep.2014.03.018