Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
19 Jun 2024
19 Jun 2024
Historique:
received:
27
06
2023
accepted:
28
05
2024
medline:
20
6
2024
pubmed:
20
6
2024
entrez:
19
6
2024
Statut:
aheadofprint
Résumé
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70-Ku80 heterodimer (Ku), X-ray repair cross complementing 4 (XRCC4) in complex with DNA ligase 4 (X4L4) and XRCC4-like factor (XLF) form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were recently obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at residue resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs lead to the formation of XLF and X4L4 condensates in vitro, which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome-editing strategies.
Identifiants
pubmed: 38898102
doi: 10.1038/s41594-024-01339-x
pii: 10.1038/s41594-024-01339-x
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Zhao, B., Rothenberg, E., Ramsden, D. A. & Lieber, M. R. The molecular basis and disease relevance of non-homologous DNA end joining. Nat. Rev. Mol. Cell Biol. 21, 765–781 (2020).
pubmed: 33077885
pmcid: 8063501
doi: 10.1038/s41580-020-00297-8
Chaplin, A. K. & Blundell, T. L. Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining. Curr. Opin. Struct. Biol. 61, 9–16 (2020).
pubmed: 31733599
doi: 10.1016/j.sbi.2019.09.008
Stinson, B. M. & Loparo, J. J. Repair of DNA double-strand breaks by the nonhomologous end joining pathway. Ann. Rev. Biochem. 90, 137–164 (2021).
pubmed: 33556282
doi: 10.1146/annurev-biochem-080320-110356
Graham, T. G. W., Carney, S. M., Walter, J. C. & Loparo, J. J. A single XLF dimer bridges DNA ends during nonhomologous end joining. Nat. Struct. Mol. Biol. 25, 877–884 (2018).
pubmed: 30177755
pmcid: 6128732
doi: 10.1038/s41594-018-0120-y
Walker, J. R., Corpina, R. A. & Goldberg, J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412, 607–614 (2001).
pubmed: 11493912
doi: 10.1038/35088000
Wang, J. L. et al. Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat. Struct. Mol. Biol. 25, 482–487 (2018).
pubmed: 29786079
pmcid: 5990469
doi: 10.1038/s41594-018-0065-1
Zhao, B. et al. The essential elements for the noncovalent association of two DNA ends during NHEJ synapsis. Nat. Commun. 10, 3588 (2019).
pubmed: 31399561
pmcid: 6688983
doi: 10.1038/s41467-019-11507-z
Chen, S. et al. Structural basis of long-range to short-range synaptic transition in NHEJ. Nature 593, 294–298 (2021).
pubmed: 33854234
pmcid: 8122075
doi: 10.1038/s41586-021-03458-7
Cisneros-Aguirre, M., Lopezcolorado, F. W., Tsai, L. J., Bhargava, R. & Stark, J. M. The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened. Nat. Commun. 13, 1–17 (2022).
doi: 10.1038/s41467-022-31365-6
Chaplin, A. K. et al. Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Mol. Cell 81, 3400–3409 (2021).
pubmed: 34352203
pmcid: 9006396
doi: 10.1016/j.molcel.2021.07.005
Chen, S., Lees-Miller, J. P., He, Y. & Lees-Miller, S. P. Structural insights into the role of DNA-PK as a master regulator in NHEJ. Genome Instab. Dis. 2, 195–210 (2021).
pubmed: 34723130
pmcid: 8549938
doi: 10.1007/s42764-021-00047-w
Liu, L. et al. Autophosphorylation transforms DNA-PK from protecting to processing DNA ends. Mol. Cell 82, 177–189 (2022).
pubmed: 34936881
doi: 10.1016/j.molcel.2021.11.025
Watanabe, G., Lieber, M. R. & Williams, D. R. Structural analysis of the basal state of the Artemis:DNA-PKcs complex. Nucleic Acids Res. 50, 7697–7720 (2022).
pubmed: 35801871
pmcid: 9303282
doi: 10.1093/nar/gkac564
Watanabe, G. & Lieber, M. R. The flexible and iterative steps within the NHEJ pathway. Prog. Biophys. Mol. Biol. 180-181, 105–119 (2023).
pubmed: 37150451
doi: 10.1016/j.pbiomolbio.2023.05.001
Amin, H., Zahid, S., Hall, C. & Chaplin, A. K. Cold snapshots of DNA repair: cryo-EM structures of DNA-PKcs and NHEJ machinery. Prog. Biophys. Mol. Biol. 186, 1–13 (2024).
pubmed: 38036101
doi: 10.1016/j.pbiomolbio.2023.11.007
Vogt, A., He, Y. & Lees-Miller, S. P. How to fix DNA breaks: new insights into the mechanism of non-homologous end joining. Biochem. Soc. Trans. 51, 1789–1800 (2023).
pubmed: 37787023
pmcid: 10657183
doi: 10.1042/BST20220741
Carney, S. M. et al. XLF acts as a flexible connector during non-homologous end joining. eLife 9, e61920 (2020).
pubmed: 33289484
pmcid: 7744095
doi: 10.7554/eLife.61920
Normanno, D. et al. Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining. eLife 6, e22900 (2017).
pubmed: 28500754
pmcid: 5468090
doi: 10.7554/eLife.22900
Grawunder, U., Zimmer, D., Kulesza, P. & Lieber, M. R. Requirement for an interaction of XRCC4 with DNA ligase IV for wild-type V(D)J recombination and DNA double-strand break repair in vivo. J. Biol. Chem. 273, 24708–24714 (1998).
pubmed: 9733770
doi: 10.1074/jbc.273.38.24708
Modesti, M., Hesse, J. E. & Gellert, M. DNA binding of XRCC4 protein is associated with V(D)J recombination but not with stimulation of DNA ligase IV activity. EMBO J. 18, 2008–2018 (1999).
pubmed: 10202163
pmcid: 1171285
doi: 10.1093/emboj/18.7.2008
Andres, S. N. et al. A human XRCC4–XLF complex bridges DNA. Nucleic Acids Res. 40, 1868–1878 (2012).
pubmed: 22287571
pmcid: 3287209
doi: 10.1093/nar/gks022
Malivert, L. et al. The C-terminal domain of Cernunnos/XLF is dispensable for DNA repair in vivo. Mol. Cell. Biol. 29, 1116–1122 (2009).
pubmed: 19103754
doi: 10.1128/MCB.01521-08
Andres, S. N., Modesti, M., Tsai, C. J., Chu, G. & Junop, M. S. Crystal structure of human XLF: a twist in nonhomologous DNA end-joining. Mol. Cell 28, 1093–1101 (2007).
pubmed: 18158905
doi: 10.1016/j.molcel.2007.10.024
Yu, Y. et al. DNA-PK phosphorylation sites in XRCC4 are not required for survival after radiation or for V(D)J recombination. DNA Repair 2, 1239–1252 (2003).
pubmed: 14599745
doi: 10.1016/S1568-7864(03)00143-5
Yu, Y. et al. DNA-PK and ATM phosphorylation sites in XLF/Cernunnos are not required for repair of DNA double strand breaks. DNA Repair 7, 1680 (2008).
pubmed: 18644470
pmcid: 3350819
doi: 10.1016/j.dnarep.2008.06.015
Koch, C. A. et al. XRCC4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV. EMBO J. 23, 3874–3885 (2004).
pubmed: 15385968
pmcid: 522785
doi: 10.1038/sj.emboj.7600375
Liu, P. et al. Akt-mediated phosphorylation of XLF impairs non-homologous end-joining DNA repair. Mol. Cell 57, 648–661 (2015).
pubmed: 25661488
pmcid: 4336609
doi: 10.1016/j.molcel.2015.01.005
Junop, M. S. et al. Crystal structure of the XRCC4 DNA repair protein and implications for end joining. EMBO J. 19, 5962–5970 (2000).
pubmed: 11080143
pmcid: 305814
doi: 10.1093/emboj/19.22.5962
Bhargava, R. et al. C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains. Nat. Commun. 9, 2484 (2018).
pubmed: 29950655
pmcid: 6021437
doi: 10.1038/s41467-018-04867-5
Cabello-Lobato, M. J. et al. Microarray screening reveals two non-conventional SUMO-binding modules linked to DNA repair by non-homologous end-joining. Nucleic Acids Res. 50, 4732–4754 (2022).
pubmed: 35420136
pmcid: 9071424
doi: 10.1093/nar/gkac237
Mahaney, B. L., Lees-Miller, S. P. & Cobb, J. A. The C-terminus of Nej1 is critical for nuclear localization and non-homologous end-joining. DNA Repair 14, 9–16 (2014).
pubmed: 24369855
doi: 10.1016/j.dnarep.2013.12.002
Malivert, L. et al. Delineation of the XRCC4-interacting region in the globular head domain of cernunnos/XLF. J. Biol. Chem. 285, 26475–26483 (2010).
pubmed: 20558749
pmcid: 2924081
doi: 10.1074/jbc.M110.138156
Nemoz, C. et al. XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat. Struct. Mol. Biol. 25, 971–980 (2018).
pubmed: 30291363
pmcid: 6234012
doi: 10.1038/s41594-018-0133-6
Seif-El-Dahan, M. et al. PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Sci. Adv. 9, eadg2834 (2023).
pubmed: 37256950
pmcid: 10413649
doi: 10.1126/sciadv.adg2834
Hammel, M. et al. XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J. of Biol. Chem. 286, 32638–32650 (2011).
doi: 10.1074/jbc.M111.272641
Lu, H., Pannicke, U., Schwarz, K. & Lieber, M. R. Length-dependent binding of human XLF to DNA and stimulation of XRCC4⋅DNA ligase IV activity. J. Biol. Chem. 282, 11155–11162 (2007).
pubmed: 17317666
doi: 10.1074/jbc.M609904200
Aravind, L. AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 26, 4413–4421 (1998).
pubmed: 9742243
pmcid: 147871
doi: 10.1093/nar/26.19.4413
Rohs, R. et al. The role of DNA shape in protein–DNA recognition. Nature 461, 1248–1253 (2009).
pubmed: 19865164
pmcid: 2793086
doi: 10.1038/nature08473
Waudby, C. A., Ramos, A., Cabrita, L. D. & Christodoulou, J. Two-dimensional NMR lineshape analysis. Sci. Rep. 6, 24826 (2016).
pubmed: 27109776
pmcid: 4843008
doi: 10.1038/srep24826
Nunn, C. M., Garman, E. & Neidle, S. Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry 36, 4792–4799 (1997).
pubmed: 9125500
doi: 10.1021/bi9628228
Camacho-Zarco, A. R. et al. NMR provides unique insight into the functional dynamics and interactions of intrinsically disordered proteins. Chem. Rev. 122, 9331–9356 (2022).
pubmed: 35446534
pmcid: 9136928
doi: 10.1021/acs.chemrev.1c01023
Clore, G. M. & Iwahara, J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem. Rev. 109, 4108–4139 (2009).
pubmed: 19522502
pmcid: 2825090
doi: 10.1021/cr900033p
Wu, P.-Y. et al. Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Mol. Cell. Biol. 29, 3163–3172 (2009).
pubmed: 19332554
pmcid: 2682001
doi: 10.1128/MCB.01895-08
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022).
Yano, K.-i, Morotomi-Yano, K., Lee, K.-J. & Chen, D. J. Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF. FEBS Lett. 585, 841–846 (2011).
pubmed: 21349273
pmcid: 3066473
doi: 10.1016/j.febslet.2011.02.020
Recuero-Checa, M. A. et al. Electron microscopy of XRCC4 and the DNA ligase IV–XRCC4 DNA repair complex. DNA Repair 8, 1380–1389 (2009).
pubmed: 19837014
doi: 10.1016/j.dnarep.2009.09.007
Mani, R. S. et al. Dual modes of interaction between XRCC4 and polynucleotide kinase/phosphatase: implications for nonhomologous end joining. J. Biol. Chem. 285, 37619–37629 (2010).
pubmed: 20852255
pmcid: 2988367
doi: 10.1074/jbc.M109.058719
Jensen, M. R., Salmon, L., Nodet, G. & Blackledge, M. Defining conformational ensembles of intrinsically disordered and partially folded proteins directly from chemical shifts. J. Am. Chem. Soc. 132, 1270–1272 (2010).
pubmed: 20063887
doi: 10.1021/ja909973n
Ferrie, J. J., Karr, J. P., Tjian, R. & Darzacq, X. ‘Structure’–function relationships in eukaryotic transcription factors: the role of intrinsically disordered regions in gene regulation. Mol. Cell 82, 3970–3984 (2022).
pubmed: 36265487
doi: 10.1016/j.molcel.2022.09.021
Mittag, T. & Pappu, R. V. A conceptual framework for understanding phase separation and addressing open questions and challenges. Mol. Cell 82, 2201–2214 (2022).
pubmed: 35675815
pmcid: 9233049
doi: 10.1016/j.molcel.2022.05.018
Musacchio, A. On the role of phase separation in the biogenesis of membraneless compartments. EMBO J. 41, e109952 (2022).
pubmed: 35107832
pmcid: 8886532
doi: 10.15252/embj.2021109952
Fijen, C. & Rothenberg, E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair 105, 103170 (2021).
pubmed: 34256335
pmcid: 8364513
doi: 10.1016/j.dnarep.2021.103170
Kilic, S. et al. Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments. EMBO J. 38, 1–17 (2019).
doi: 10.15252/embj.2018101379
Thapar, R. et al. Mechanism of efficient double-strand break repair by a long non-coding RNA. Nucleic Acids Res. 48, 10953–10972 (2020).
pubmed: 33045735
pmcid: 7641761
doi: 10.1093/nar/gkaa784
Muzzopappa, F. et al. Detecting and quantifying liquid–liquid phase separation in living cells by model-free calibrated half-bleaching. Nat. Commun. 13, 7787 (2022).
pubmed: 36526633
pmcid: 9758202
doi: 10.1038/s41467-022-35430-y
Roy, S. et al. XRCC4/XLF interaction is variably required for DNA repair and is not required for ligase IV stimulation. Mol. Cell. Biol. 35, 3017–3028 (2015).
pubmed: 26100018
pmcid: 4525314
doi: 10.1128/MCB.01503-14
Love, C. et al. Reversible pH-responsive coacervate formation in lipid vesicles activates dormant enzymatic reactions. Angew. Chem. Int. Ed. Engl. 59, 5950–5957 (2020).
pubmed: 31943629
pmcid: 7187140
doi: 10.1002/anie.201914893
Peeples, W. & Rosen, M. K. Mechanistic dissection of increased enzymatic rate in a phase-separated compartment. Nat. Chem. Biol. 17, 693–702 (2021).
pubmed: 34035521
pmcid: 8635274
doi: 10.1038/s41589-021-00801-x
Banani, S. F. et al. Compositional control of phase-separated cellular bodies. Cell 166, 651–663 (2016).
pubmed: 27374333
pmcid: 4967043
doi: 10.1016/j.cell.2016.06.010
Ruff, K. M., Dar, F. & Pappu, R. V. Ligand effects on phase separation of multivalent macromolecules. Proc. Natl Acad. Sci. USA 118, e2017184118 (2021).
pubmed: 33653957
pmcid: 7958451
doi: 10.1073/pnas.2017184118
Frit, P., Ropars, V., Modesti, M., Charbonnier, J. B. & Calsou, P. Plugged into the Ku–DNA hub: the NHEJ network. Prog. Biophys. Mol. Biol. 147, 62–76 (2019).
pubmed: 30851288
doi: 10.1016/j.pbiomolbio.2019.03.001
Costantini, S., Woodbine, L., Andreoli, L., Jeggo, P. A. & Vindigni, A. Interaction of the Ku heterodimer with the DNA ligase IV/XRCC4 complex and its regulation by DNA-PK. DNA Repair 6, 712–722 (2007).
pubmed: 17241822
doi: 10.1016/j.dnarep.2006.12.007
Charlier, C. et al. Structure and dynamics of an intrinsically disordered protein region that partially folds upon binding by chemical-exchange NMR. J. Am. Chem. Soc. 139, 12219–12227 (2017).
pubmed: 28780862
doi: 10.1021/jacs.7b05823
De Ioannes, P., Malu, S., Cortes, P. & Aggarwal, A. K. Structural basis of DNA ligase IV–Artemis interaction in nonhomologous end-joining. Cell Rep. 2, 1505–1512 (2012).
pubmed: 23219551
pmcid: 3538150
doi: 10.1016/j.celrep.2012.11.004
Malu, S. et al. Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA ligase IV and DNA-PKcs. J. Exp. Med. 209, 955–963 (2012).
pubmed: 22529269
pmcid: 3348108
doi: 10.1084/jem.20111437
Ochi, T., Gu, X. & Blundell, T. L. Structure of the catalytic region of DNA ligase IV in complex with an Artemis fragment sheds light on double-strand break repair. Structure 21, 672–679 (2013).
pubmed: 23523427
pmcid: 3664939
doi: 10.1016/j.str.2013.02.014
Dignon, G. L., Best, R. B. & Mittal, J. Biomolecular phase separation: from molecular driving forces to macroscopic properties. Ann. Rev. Phys. Chem. 71, 53–75 (2020).
doi: 10.1146/annurev-physchem-071819-113553
Kim, K. et al. Ligand binding characteristics of the Ku80 von Willebrand domain. DNA Repair 85, 102739 (2020).
pubmed: 31733588
doi: 10.1016/j.dnarep.2019.102739
Hammel, M. & Tainer, J. A. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci. 30, 1735–1756 (2021).
pubmed: 34056803
pmcid: 8376411
doi: 10.1002/pro.4133
Shoemaker, B. A., Portman, J. J. & Wolynes, P. G. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl Acad. Sci. USA 97, 8868–8873 (2000).
pubmed: 10908673
pmcid: 16787
doi: 10.1073/pnas.160259697
Hammel, M. et al. Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J. Biol. Chem. 285, 1414–1423 (2010).
pubmed: 19893054
doi: 10.1074/jbc.M109.065615
Quail, T. et al. Force generation by protein–DNA co-condensation. Nat. Phys. 17, 1007–1012 (2021).
doi: 10.1038/s41567-021-01285-1
Berg, E. et al. XRCC4 controls nuclear import and distribution of ligase IV and exchanges faster at damaged DNA in complex with ligase IV. DNA Repair 10, 1232–1242 (2011).
pubmed: 21982441
doi: 10.1016/j.dnarep.2011.09.012
Yano, K. et al. Ku recruits XLF to DNA double-strand breaks. EMBO Rep. 9, 91–96 (2008).
pubmed: 18064046
doi: 10.1038/sj.embor.7401137
Reid, D. A. et al. Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair. Proc. Natl Acad. Sci. USA 112, E2575–E2584 (2015).
pubmed: 25941401
pmcid: 4443322
doi: 10.1073/pnas.1420115112
Oksenych, V. et al. Functional redundancy between repair factor XLF and damage response mediator 53BP1 in V(D)J recombination and DNA repair. Proc. Natl Acad. Sci. USA 109, 2455–2460 (2012).
pubmed: 22308489
pmcid: 3289340
doi: 10.1073/pnas.1121458109
Pessina, F. et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 21, 1286–1299 (2019).
pubmed: 31570834
pmcid: 6859070
doi: 10.1038/s41556-019-0392-4
Knott, G. J., Bond, C. S. & Fox, A. H. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res. 44, 3989–4004 (2016).
pubmed: 27084935
pmcid: 4872119
doi: 10.1093/nar/gkw271
Jaafar, L., Li, Z., Li, S. & Dynan, W. S. 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 (2017).
pubmed: 27924002
doi: 10.1093/nar/gkw1209
González-Prieto, R. et al. Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex. Cell Rep. 34, 108691 (2021).
pubmed: 33503430
doi: 10.1016/j.celrep.2021.108691
Hammel, M. et al. An intrinsically disordered APLF links Ku, DNA-PKcs, and XRCC4–DNA ligase IV in an extended flexible non-homologous end joining complex. J. Biol. Chem. 291, 26987–27006 (2016).
pubmed: 27875301
pmcid: 5207133
doi: 10.1074/jbc.M116.751867
Unfried, J. P. et al. Long noncoding RNA NIHCOLE promotes ligation efficiency of DNA double-strand breaks in hepatocellular carcinoma. Cancer Res. 81, 4910–4925 (2021).
pubmed: 34321241
pmcid: 8488005
doi: 10.1158/0008-5472.CAN-21-0463
Li, P. et al. Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340 (2012).
pubmed: 22398450
pmcid: 3343696
doi: 10.1038/nature10879
Hardwick, S. W. et al. Cryo-EM structure of a DNA-PK trimer: higher order oligomerisation in NHEJ. Structure 31, 895–902 (2023).
pubmed: 37311458
doi: 10.1016/j.str.2023.05.013
Mittag, T. & Fawzi, N. L. Protein quality and miRNA slicing get into phase. Nat. Cell Biol. 20, 635–637 (2018).
pubmed: 29802409
doi: 10.1038/s41556-018-0113-4
Sheu-Gruttadauria, J. & MacRae, I. J. Phase transitions in the assembly and function of human miRISC. Cell 173, 946–957 (2018).
pubmed: 29576456
pmcid: 5935535
doi: 10.1016/j.cell.2018.02.051
Dao, T. P. et al. Ubiquitin modulates liquid–liquid phase separation of UBQLN2 via disruption of multivalent interactions. Mol. Cell 69, 965–978 (2018).
pubmed: 29526694
pmcid: 6181577
doi: 10.1016/j.molcel.2018.02.004
Kumar, V., Alt, F. W. & Frock, R. L. PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. Proc. Natl Acad. Sci. USA 113, 10619–10624 (2016).
pubmed: 27601633
pmcid: 5035843
doi: 10.1073/pnas.1611882113
Liu, X. et al. Overlapping functions between XLF repair protein and 53BP1 DNA damage response factor in end joining and lymphocyte development. Proc. Natl Acad. Sci. USA 109, 3903–3908 (2012).
pubmed: 22355127
pmcid: 3309750
doi: 10.1073/pnas.1120160109
Oksenych, V. et al. Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining. Proc. Natl Acad. Sci. USA 110, 2234–2239 (2013).
pubmed: 23345432
pmcid: 3568359
doi: 10.1073/pnas.1222573110
Zha, S. et al. ATM damage response and XLF repair factor are functionally redundant in joining DNA breaks. Nature 469, 250–254 (2011).
pubmed: 21160472
doi: 10.1038/nature09604
Vítor, A. C., Huertas, P., Legube, G. & de Almeida, S. F. Studying DNA double-strand break repair: an ever-growing toolbox. Front. Mol. Biosci. 7, 24 (2020).
pubmed: 32154266
pmcid: 7047327
doi: 10.3389/fmolb.2020.00024
& Goff, N. J. Catalytically inactive DNA ligase IV promotes DNA repair in living cells. Nucleic Acids Res. 50, 11058–11071 (2022).
pubmed: 36263813
pmcid: 9638927
doi: 10.1093/nar/gkac913
Marley, J., Lu, M. & Bracken, C. A method for efficient isotopic labeling of recombinant proteins. J. Biomol. NMR 20, 71–75 (2001).
pubmed: 11430757
doi: 10.1023/A:1011254402785
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Bhargava, R., Lopezcolorado, F. W., Jillianne Tsai, L. & Stark, J. M. The canonical non-homologous end joining factor XLF promotes chromosomal deletion rearrangements in human cells. J. Biol. Chem. 295, 125–137 (2020).
pubmed: 31753920
doi: 10.1074/jbc.RA119.010421
Stark, J. M., Pierce, A. J., Oh, J., Pastink, A. & Jasin, M. Genetic steps of mammalian homologous repair with distinct mutagenic consequences. Mol. Cell. Biol. 24, 9305–9316 (2004).
pubmed: 15485900
pmcid: 522275
doi: 10.1128/MCB.24.21.9305-9316.2004
Gunn, A. & Stark, J. M. I-SceI-based assays to examine distinct repair outcomes of mammalian chromosomal double strand breaks. Methods Mol. Biol. 920, 379–391 (2012).
pubmed: 22941618
doi: 10.1007/978-1-61779-998-3_27
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).
pubmed: 8520220
doi: 10.1007/BF00197809
Lee, W., Tonelli, M. & Markley, J. L. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31, 1325–1327 (2015).
pubmed: 25505092
doi: 10.1093/bioinformatics/btu830
Favier, A. & Brutscher, B. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers. J. Biomol. NMR 73, 199–211 (2019).
pubmed: 31076970
doi: 10.1007/s10858-019-00249-1
Solyom, Z. et al. BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins. J. Biomol. NMR 55, 311–321 (2013).
pubmed: 23435576
doi: 10.1007/s10858-013-9715-0
Schanda, P., Van Melckebeke, H. & Brutscher, B. Speeding up three-dimensional protein NMR experiments to a few minutes. J. Am. Chem. Soc. 128, 9042–9043 (2006).
pubmed: 16834371
doi: 10.1021/ja062025p
Kay, L. E., Nicholson, L. K., Delaglio, F., Bax, A. & Torchia, D. A. Pulse sequences for removal of the effects of cross correlation between dipolar and chemical-shift anisotropy relaxation mechanisms on the measurement of heteronuclear T
Ferrage, F. Protein dynamics by
pubmed: 22167673
doi: 10.1007/978-1-61779-480-3_9
Ferrage, F., Reichel, A., Battacharya, S., Cowburn, D. & Ghose, R. On the measurement of
pubmed: 20951618
pmcid: 3638772
doi: 10.1016/j.jmr.2010.09.014
Waudby, C. A. & Christodoulou, J. NMR lineshape analysis of intrinsically disordered protein interactions. Methods Mol. Biol. 2141, 477–504 (2020).
pubmed: 32696373
pmcid: 7116509
doi: 10.1007/978-1-0716-0524-0_24