MULTIFUNCTIONAL SFPQ PROTEIN: ROLE IN DOUBLE-STRANDED DNA BREAK REPAIR
- Authors: Agapkina Y.Y.1,2, Silkina M.O1, Kikhai T.F1, Gottikh M.B1,2
-
Affiliations:
- Faculty of Chemistry, Lomonosov Moscow State University
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
- Issue: Vol 90, No 10 (2025)
- Pages: 1425-1438
- Section: Articles
- URL: https://journals.rcsi.science/0320-9725/article/view/355110
- DOI: https://doi.org/10.31857/S0320972525100024
- ID: 355110
Cite item
Abstract
About the authors
Yu. Yu Agapkina
Faculty of Chemistry, Lomonosov Moscow State University; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia; Moscow, Russia
M. O Silkina
Faculty of Chemistry, Lomonosov Moscow State UniversityMoscow, Russia
T. F Kikhai
Faculty of Chemistry, Lomonosov Moscow State University
Email: kih.t1996@yandex.ru
Moscow, Russia
M. B Gottikh
Faculty of Chemistry, Lomonosov Moscow State University; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
Email: gottikh@belozersky.msu.ru
Moscow, Russia; Moscow, Russia
References
- Thandapani, P., O'Connor, T. R., Bailey, T. L., and Richard, S. (2013) Defining the RGG/RG motif, Mol. Cell, 50, 613-623, https://doi.org/10.1016/j.molcel.2013.05.021.
- Rosonina, E., Ip, J. Y., Calarco, J. A., Bakowski, M. A., Emili, A., McCracken, S., Tucker, P., Ingles, C. J., and Blencowe, B. J. (2005) Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo, Mol. Cell. Biol., 25, 6734-6746, https://doi.org/10.1128/MCB.25.15.6734-6746.2005.
- Knott, G. J., Bond, C. S., and Fox, A. H. (2016) The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold, Nucleic Acids Res., 44, 3989-4004, https://doi.org/10.1093/nar/gkw271.
- Niu, X., Zhang, L., Wu, Y., Zong, Z., Wang, B., Liu, J., et al. (2023) Biomolecular condensates: formation mechanisms, biological functions, and therapeutic targets, MedComm., 4, e223, https://doi.org/10.1002/mco2.223.
- McCluggage, F., and Fox, A. H. (2021) Paraspeckle nuclear condensates: global sensors of cell stress? Bioessays, 43, e2000245, https://doi.org/10.1002/bies.202000245.
- Marshall, A. C., Cummins, J., Kobelke, S., Zhu, T., Widagdo, J., Anggono, V., Hyman, A., Fox, A. H., Bond, C. S., and Lee, M. (2023) Different low-complexity regions of SFPQ play distinct roles in the formation of biomolecular condensates, J. Mol. Biol., 435, 168364, https://doi.org/10.1016/j.jmb.2023.168364.
- Heyd, E., and Lynch, K. W. (2011) PSF controls expression of histone variants and cellular viability in thymocytes, Biochem. Biophys. Res. Commun., 414, 743-749, https://doi.org/10.1016/j.bbrc.2011.09.149.
- Melton, A. A., Jackson, J., Wang, J., and Lynch, K. W. (2007) Combinatorial control of signal-induced exon repression by hnRNP L and PSF, Mol. Cell. Biol., 27, 6972-6984, https://doi.org/10.1128/MCB.00419-07.
- Ke, Y. D., Dramiga, J., Schutz, U., Kril, J. J., Ittner, L. M., Schroder, H., and Gotz, J. (2012) Tau-mediated nuclear depletion and cytoplasmic accumulation of SFPQ in Alzheimer's and Pick's disease, PLoS One, 7, e35678, https://doi.org/10.1371/journal.pone.0035678.
- Stamova, B.S., Tian, Y., Nordahl, C. W., Shen, M. D., Rogers, S., Amaral, D. G., and Sharp, F. R. (2013) Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders, Mol. Autism, 4, 30, https://doi.org/10.1186/2040-2392-4-30.
- Jiang, F. N., He, H. C., Zhang, Y.Q., Yang, D. L., Huang, J. H., Zhu, Y. X., Mo, R. J., Chen, G., Yang, S. B., Chen, Y. R., Zhong, W. D., and Zhou, W. L. (2013) An integrative proteomics and interaction network-based classifier for prostate cancer diagnosis, PLoS One, 8, e63941, https://doi.org/10.1371/journal.pone.0063941.
- Gozani, O., Patton, J. G., and Reed, R. (1994) A novel set of spliceosome-associated proteins and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction, EMBO J., 13, 3356-3367, https://doi.org/10.1002/j.1460-2075.1994.tb06638.x.
- Dong, X., Sweet, J., Challis, J. R., Brown, T., and Lye, S. J. (2007) Transcriptional activity of androgen receptor is modulated by two RNA splicing factors, PSF and p54nrb, Mol. Cell. Biol., 27, 4863-4875, https://doi.org/10.1128/MCB.02144-06.
- Lim, Y. W., James, D., Huang, J., and Lee, M. (2020) The emerging role of the RNA-binding protein SFPQ in neuronal function and neurodegeneration, Int. J. Mol. Sci., 21, 7151, https://doi.org/10.3390/ijms21197151.
- Kikhai, T., Agapkina, Y., Silkina, M., Prikazchikova, T., and Gottikh, M. (2024) The cellular SFPQ protein as a positive factor in the HIV-1 integration, Biochimie, 222, 9-17, https://doi.org/10.1016/j.biochi.2024.02.002.
- Shadrina, O. A., Kikhay, T. F., Agapkina, Y. Y., and Gottikh, M. B. (2022) SFPQ and NONO proteins and long non-coding NEAT1 RNA: cellular functions and role in the HIV-1 life cycle, Mol. Biol., 56, 196-209, https://doi.org/10.31857/S0026898422020161.
- Milcamps, R., and Michiels, T. (2024) Involvement of paraspeckle components in viral infections, Nucleus, 15, 2350178, https://doi.org/10.1080/19491034.2024.2350178.
- Yu, D., Huang, C. J., and Tucker, H. O. (2024) Established and evolving roles of the Multifunctional non-POU domain-containing octamer-binding protein (NonO) and splicing factor proline- and glutamine-rich (SFPQ), J. Dev. Biol., 12, 3, https://doi.org/10.3390/jdb12010003.
- Takeiwa, T., Ikeda, K., Horie, K., and Inoue, S. (2024) Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer, RNA Biol., 21, 1-17, https://doi.org/10.1080/15476286.2024.2332855.
- Harrison, J. C., and Haber, J. E. (2006) Surviving the breakup: the DNA damage checkpoint, Annu. Rev. Genet., 40, 209-235, https://doi.org/10.1146/annurev.genet.40.051206.105231.
- Khanna, A. (2015) DNA damage in cancer therapeutics: a boon or a curse? Cancer Res., 75, 2133-2138, https://doi.org/10.1158/0008-5472.CAN-14-3247.
- Iyama, T., and Wilson, D. M. 3rd. (2013) DNA repair mechanisms in dividing and non-dividing cells, DNA Repair (Amst), 12, 620-636, https://doi.org/10.1016/j.dnarep.2013.04.015.
- Wyman, C., and Kanaar, R. (2006) DNA double-strand break repair: all's well that ends well, Annu. Rev. Genet., 40, 363-383, https://doi.org/10.1146/annurev.genet.40.110405.090451.
- Lieber, M. R. (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway, Annu. Rev. Biochem., 79, 181-211, https://doi.org/10.1146/annurev.biochem.052308.093131.
- Scully, R., Panday, A., Elango, R., and Willis, N. A. (2019) DNA double-strand break repair-pathway choice in somatic mammalian cells, Nat. Rev. Mol. Cell Biol., 20, 698-714, https://doi.org/10.1038/s41580-019-0152-0.
- Shiloh, Y. (2006) The ATM-mediated DNA-damage response: taking shape, Trends Biochem. Sci., 31, 402-410, https://doi.org/10.1016/j.tibs.2006.05.004.
- Weterings, E., and Chen, D. J. (2007) DNA-dependent protein kinase in nonhomologous end joining: a lock with multiple keys? J. Cell Biol., 179, 183-186, https://doi.org/10.1083/jcb.200705106.
- Cimprich, K.A., and Cortez, D. (2008) ATR: an essential regulator of genome integrity, Nat. Rev. Mol. Cell Biol., 9, 616-627, https://doi.org/10.1038/nrm2450.
- Falck, J., Coates, J., and Jackson, S. P. (2005) Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage, Nature, 434, 605-611, https://doi.org/10.1038/nature03442.
- Stucki, M., and Jackson, S. P. (2006) gammaH2AX and MDC1: anchoring the DNA-damage-response machinery to broken chromosomes, DNA Repair, 5, 534-543, https://doi.org/10.1016/j.dnarep.2006.01.012.
- Graham, T. G., Walter, J. C., and Loparo, J. J. (2016) Two-stage synapsis of DNA ends during non-homologous end joining, Mol. Cell, 61, 850-858, https://doi.org/10.1016/j.molcel.2016.02.010.
- Goodarzi, A. A., and Jeggo, P. A. (2012) The heterochromatic barrier to DNA double strand break repair: how to get the entry visa, Int. J. Mol. Sci., 13, 11844-11860, https://doi.org/10.3390/ijms130911844.
- Syed, A., and Tainer, J. A. (2018) The MRE11-RAD50-NBS1 complex conducts the orchestration of damage signaling and outcomes to stress in DNA replication and repair, Annu. Rev. Biochem., 87, 263-294, https://doi.org/10.1146/annurev-biochem-062917-012415.
- Daley, J. M., Kwon, Y., Niu, H., and Sung, P. (2013) Investigations of homologous recombination pathways and their regulation, Yale J. Biol. Med., 86, 453-461.
- Alemasova, E. E., and Lavrik, O. I. (2019) Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins, Nucleic Acids Res., 47, 3811-3827, https://doi.org/10.1093/nar/gkz120.
- Polo, S. E., and Jackson, S. P. (2011) Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications, Genes Dev., 25, 409-433, https://doi.org/10.1101/gad.2021311.
- Dantzer, F., de La Rubia, G., Menissier-De Murcia, J., Hostomsky, Z., de Murcia, G., and Schreiber, V. (2000) Base excision repair is impaired in mammalian cells lacking poly(ADP-ribose) polymerase-1, Biochemistry, 39, 7559-7569, https://doi.org/10.1021/bi000442k.
- Spiegel, J. O., Van Houten, B., and Durrant, J. D. (2021) PARP1: structural insights and pharmacological targets for inhibition, DNA Repair (Amst), 103, 103125, https://doi.org/10.1016/j.dnarep.2021.103125.
- De Vos, M., Schreiber, V., and Dantzer, F. (2012) The diverse roles and clinical relevance of PARPs in DNA damage repair: current state of the art, Biochem. Pharmacol., 84, 137-146, https://doi.org/10.1016/j.bcp.2012.03.018.
- Bladen, C. L., Udayakumar, D., Takeda, Y., and Dynan, W. S. (2005) Identification of the polypyrimidine tract binding protein-associated splicing factor-p54(nrb) complex as a candidate DNA double-strand break rejoining factor, J. Biol. Chem., 280, 5205-5210, https://doi.org/10.1074/jbc.M412758200.
- Rajesh, C., Baker, D. K., Pierce, A. J., and Pittman, D. L. (2011) The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion, Nucleic Acids Res., 39, 132-145, https://doi.org/10.1093/nar/gkq738.
- Smiraldo, P. G., Gruver, A. M., Osborn, J. C., and Pittman, D. L. (2005) Extensive chromosomal instability in Rad51d-deficient mouse cells, Cancer Res., 65, 2089-2096, https://doi.org/10.1158/0008-5472.CAN-04-2079.
- Godthelp, B. C., Wiegant, W. W., van Duijn-Goedhart, A., Scharer, O. D., van Buul, P. P., Kanaar, R., and Zdzienicka, M. Z. (2002) Mammalian Rad51C contributes to DNA cross-link resistance, sister chromatid cohesion and genomic stability, Nucleic Acids Res., 30, 2172-2182, https://doi.org/10.1093/nar/30.10.2172.
- Salton, M., Lerenthal, Y., Wang, S. Y., Chen, D. J., and Shiloh, Y. (2010) Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response, Cell Cycle, 9, 1568-1576, https://doi.org/10.4161/cc.9.8.11298.
- FitzGerald, J. E., Grenon, M., and Lowndes, N. F. (2009) 53BP1: function and mechanisms of focal recruitment, Biochem. Soc. Trans., 37, 897-904, https://doi.org/10.1042/BST0370897.
- Ha, K., Takeda, Y., and Dynan, W. S. (2011) Sequences in PSF/SFPQ mediate radioresistance and recruitment of PSF/SFPQ-containing complexes to DNA damage sites in human cells, DNA Repair (Amst), 10, 252-259, https://doi.org/10.1016/j.dnarep.2010.11.009.
- Morozumi, Y., Takizawa, Y., Takaku, M., and Kurumizaka, H. (2009) Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities, Nucleic Acids Res., 37, 4296-4307, https://doi.org/10.1093/nar/gkp298.
- Udayakumar, D., and Dynan, W. S. (2015) Characterization of DNA binding and pairing activities associated with the native SFPQ-NONO DNA repair protein complex, Biochem. Biophys. Res. Commun., 463, 473-478, https://doi.org/10.1016/j.bbrc.2015.05.024.
- Jaafar, L., Li, Z., Li, S., and Dynan, W. S. (2017) SFPQ-NONO and XLF function separately and together to promote DNA double-strand break repair via canonical nonhomologous end joining, Nucleic Acids Res., 45, 1848-1859, https://doi.org/10.1093/nar/gkw1209.
- Levone, B. R., Lenzken, S. C., Antonaci, M., Maiser, A., Rapp, A., Conte, F., Reber, S., Mechtersheimer, J., Ronchi, A. E., Muhlemann, O., Leonhardt, H., Cardoso, M. C., Ruepp, M. D., and Barabino, S. M. L. (2021) FUS-dependent liquid-liquid phase separation is important for DNA repair initiation, J. Cell Biol., 220, e202008030, https://doi.org/10.1083/jcb.202008030.
- Morchikh, M., Cribier, A., Raffel, R., Amraoui, S., Cau, J., Severac, D., Dubois, E., Schwartz, O., Bennasser, Y., and Benkirane, M. (2017) HEXIM1 and NEAT1 long non-coding RNA form a multi-subunit complex that regulates DNA-mediated innate immune response, Mol. Cell, 67, 387-399.e5, https://doi.org/10.1016/j.molcel.2017.06.020.
- Mastrocola, A. S., Kim, S. H., Trinh, A. T., Rodenkirch, L. A., and Tibbetts, R. S. (2013) The RNA-binding protein fused in sarcoma (FUS) functions downstream of poly(ADP-ribose) polymerase (PARP) in response to DNA damage, J. Biol. Chem., 288, 24731-24741, https://doi.org/10.1074/jbc.M113.497974.
- Aleksandrov, R., Dotchev, A., Poser, I., Krastev, D., Georgiev, G., Panova, G., Babukov, Y., Danovski, G., Dyankova, T., Hubatsch, L., Ivanova, A., Atemin, A., Nedelcheva-Veleva, M. N., Hasse, S., Sarov, M., Buchholz, F., Hyman, A. A., Grill, S. W., and Stoynov, S. S. (2018) Protein dynamics in complex DNA lesions, Mol. Cell, 69, 1046-1061.e6, https://doi.org/10.1016/j.molcel.2018.02.016.
- Wang, J. C. (2002) Cellular roles of DNA topoisomerases: a molecular perspective, Nat. Rev. Mol. Cell Biol., 3, 430-440, https://doi.org/10.1038/nrm831.
- Morimoto, S., Tsuda, M., Bunch, H., Sasanuma, H., Austin, C., and Takeda, S. (2019) Type II DNA topoisomerases cause spontaneous double-strand breaks in genomic DNA, Genes (Basel), 10, 868, https://doi.org/10.3390/genes10110868.
- Straub, T., Grue, P., Uhse, A., Lisby, M., Knudsen, B. R., Tange, T. O., Westergaard, O., and Boege, F. (1998) The RNA-splicing factor PSF/p54 controls DNA-topoisomerase I activity by a direct interaction, J. Biol. Chem., 273, 26261-26266, https://doi.org/10.1074/jbc.273.41.26261.
- Kawano, S., Miyaji, M., Ichiyasu, S., Tsutsui, K. M., and Tsutsui, K. (2010) Regulation of DNA topoisomerase IIbeta through RNA-dependent association with heterogeneous nuclear ribonucleoprotein U (hnRNP U), J. Biol. Chem., 285, 26451-26460, https://doi.org/10.1074/jbc.M110.112979.
- Mäkiniemi, M., Hillukkala, T., Tuusa, J., Reini, K., Vaara, M., Huang, D., Pospiech, H., Majuri, I., Westerling, T., Mäkelä, T. P., and Syväoja, J. E. (2001) BRCT domain-containing protein TopBP1 functions in DNA replication and damage response, J. Biol. Chem., 276, 30399-30406, https://doi.org/10.1074/jbc.M102245200.
- Kuhnert, A., Schmidt, U., Monajembashi, S., Franke, C., Schlott, B., Grosse, F., Greulich, K. O., Saluz, H. P., and Hanel, F. (2012) Proteomic identification of PSF and p54(nrb) as TopBP1-interacting proteins, J. Cell. Biochem., 113, 1744-1753, https://doi.org/10.1002/jcb.24045.
- Lin, M. Z., Marzec, K. A., Martin, J. L., and Baxter, R. C. (2014) The role of insulin-like growth factor binding protein-3 in the breast cancer cell response to DNA-damaging agents, Oncogene, 33, 85-96, https://doi.org/10.1038/onc.2012.538.
- De Silva, H.C., Lin, M. Z., Phillips, L., Martin, J. L., and Baxter, R. C. (2019) IGFBP-3 interacts with NONO and SFPQ in PARP-dependent DNA damage repair in triple-negative breast cancer, Cell. Mol. Life Sci., 76, 2015-2030, https://doi.org/10.1007/s00018-019-03033-4.
- Zhang, Y., He, Q., Hu, Z., Feng, Y., Fan, L., Tang, Z., Yuan, J., Shan, W., Li, C., Hu, X., Tanyi, J. L., Fan, Y., Huang, Q., Montone, K., Dang, C. V., and Zhang, L. (2016) Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer, Nat. Struct. Mol. Biol., 23, 522-530, https://doi.org/10.1038/nsmb.3211.
- Masson, J. Y., and West, S. C. (2001) The Rad51 and Dmc1 recombinases: a non-identical twin relationship, Trends Biochem. Sci., 26, 131-136, https://doi.org/10.1016/s0968-0004(00)01742-4.
- West, S. C. (2003) Molecular views of recombination proteins and their control, Nat. Rev. Mol. Cell Biol., 4, 435-445, https://doi.org/10.1038/nrm1127.
- Morozumi, Y., Ino, R., Takaku, M., Hosokawa, M., Chuma, S., and Kurumizaka, H. (2012) Human PSF concentrates DNA and stimulates duplex capture in DMC1-mediated homologous pairing, Nucleic Acids Res., 40, 3041-3051, https://doi.org/10.1093/nar/gkr1229.
- Peng, D., Luo, L., Zhang, X., Wei, C., Zhang, Z., and Han, L. (2022) CircRNA: An emerging star in the progression of glioma, Biomed. Pharmacother., 151, 113150, https://doi.org/10.1016/j.biopha.2022.113150.
- Peng, D., Wei, C., Jing, B., Yu, R., Zhang, Z., and Han, L. (2024) A novel protein encoded by circCOPA inhibits the malignant phenotype of glioblastoma cells and increases their sensitivity to temozolomide by disrupting the NONO-SFPQ complex, Cell Death Dis., 15, 616, https://doi.org/10.1038/s41419-024-07010-z.
- Dianatpour, A., and Ghafouri-Fard, S. (2017) The role of long non coding RNAs in the repair of DNA double strand breaks, Int. J. Mol. Cell. Med., 6, 1-12, https://doi.org/10.22088/acadpub.BUMS.6.1.1.
- Wu, Z., and Wang, Y. (2017) Studies of lncRNAs in DNA double strand break repair: what is new? Oncotarget, 6, 102690-102704, https://doi.org/10.18632/oncotarget.22090.
- Cheng, Y., Han, R., Wang, M., Wang, S., Zhou, J., Wang, J., and Xu, H. (2025) M6A-mediated lncRNA SCIRT stability promotes NSCLC progression through binding to SFPQ and activating the PI3K/Akt pathway, Cell. Mol. Life Sci., 82, 63, https://doi.org/10.1007/s00018-025-05594-z.
- Fu, W., Ren, H., Shou, J., Liao, Q., Li, L., Shi, Y., Jose, P. A., Zeng, C., and Wang, W. E. (2022) Loss of NPPA-AS1 promotes heart regeneration by stabilizing SFPQ-NONO heteromer-induced DNA repair, Basic Res. Cardiol., 117, 10, https://doi.org/10.1007/s00395-022-00921-y.
- Sun, N., Chen, Q., Chen, H., Sun, P., Liu, Y., Song, D., Yu, D., Wang, P., Song, Y., Qin, J., Tian, K., Zhong, J., Ma, W., Xuan, H., Qian, D., Yuan, Y., Chen, T., Wang, X., Jiang, C., Cai, J., and Meng, X. (2025) A novel nuclear RNA HSDS2 scaffolding NONO/SFPQ complex modulates DNA damage repair to facilitate temozolomide resistance, Neuro Oncol., 27, 963-978, https://doi.org/10.1093/neuonc/noae272.
- Zhang, Y., Guan, B., Wu, Y., Du, F., Zhuang, J., Yang, Y., Guan, G., and Liu, X. (2021) LncRNAs associated with chemoradiotherapy response and prognosis in locally advanced rectal cancer, J. Inflamm. Res., 14, 6275-6292, https://doi.org/10.2147/JIR.S334096.
- Mehta, S., and Zhang, J. (2022) Liquid-liquid phase separation drives cellular function and dysfunction in cancer, Nat. Rev. Cancer., 22, 239-252, https://doi.org/10.1038/s41568-022-00444-7.
- Su, Q., Mehta, S., and Zhang, J. (2021) Liquid-liquid phase separation: orchestrating cell signaling through time and space, Mol. Cell., 81, 4137-4146, https://doi.org/10.1016/j.molcel.2021.09.010.
- Wang, Y. L., Zhao, W. W., Shi, J., Wan, X. B., Zheng, J., and Fan, X. J. (2023) Liquid-liquid phase separation in DNA double-strand breaks repair, Cell Death Dis., 14, 746, https://doi.org/10.1038/s41419-023-06267-0.
Supplementary files


