5kgf › Citations

The structural basis of modified nucleosome recognition by 53BP1.

Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien JP, McEwan A, Noordermeer SM, Sicheri F, Rubinstein JL, Durocher D
Nature 536 100-3 (2016)
Cited: 133 times
EuropePMC logo PMID: 27462807

Abstract

DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates H2A on lysine 13 and lysine 15 (refs 7, 8) (yielding H2AK13ub and H2AK15ub, respectively), an event that triggers the recruitment of 53BP1 (also known as TP53BP1) to chromatin flanking DSBs. 53BP1 binds specifically to H2AK15ub-containing nucleosomes through a peptide segment termed the ubiquitination-dependent recruitment motif (UDR), which requires the simultaneous engagement of histone H4 lysine 20 dimethylation (H4K20me2) by its tandem Tudor domain. How 53BP1 interacts with these two histone marks in the nucleosomal context, how it recognizes ubiquitin, and how it discriminates between H2AK13ub and H2AK15ub is unknown. Here we present the electron cryomicroscopy (cryo-EM) structure of a dimerized human 53BP1 fragment bound to a H4K20me2-containing and H2AK15ub-containing nucleosome core particle (NCP-ubme) at 4.5 Å resolution. The structure reveals that H4K20me2 and H2AK15ub recognition involves intimate contacts with multiple nucleosomal elements including the acidic patch. Ubiquitin recognition by 53BP1 is unusual and involves the sandwiching of the UDR segment between ubiquitin and the NCP surface. The selectivity for H2AK15ub is imparted by two arginine fingers in the H2A amino-terminal tail, which straddle the nucleosomal DNA and serve to position ubiquitin over the NCP-bound UDR segment. The structure of the complex between NCP-ubme and 53BP1 reveals the basis of 53BP1 recruitment to DSB sites and illuminates how combinations of histone marks and nucleosomal elements cooperate to produce highly specific chromatin responses, such as those elicited following chromosome breaks.

Reviews - 5kgf mentioned but not cited (4)

  1. Principles of nucleosome recognition by chromatin factors and enzymes. McGinty RK, Tan S. Curr Opin Struct Biol 71 16-26 (2021)
  2. Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications. Vaughan RM, Kupai A, Rothbart SB. Trends Biochem Sci 46 258-269 (2021)
  3. Decoding histone ubiquitylation. Chen JJ, Stermer D, Tanny JC. Front Cell Dev Biol 10 968398 (2022)
  4. Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies. Musselman CA, Kutateladze TG. ACS Chem Biol 14 579-586 (2019)

Articles - 5kgf mentioned but not cited (6)

  1. The expanding landscape of 'oncohistone' mutations in human cancers. Nacev BA, Feng L, Bagert JD, Lemiesz AE, Gao J, Soshnev AA, Kundra R, Schultz N, Muir TW, Allis CD. Nature 567 473-478 (2019)
  2. Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T. Elife 7 (2018)
  3. Acetylation of 53BP1 dictates the DNA double strand break repair pathway. Guo X, Bai Y, Zhao M, Zhou M, Shen Q, Yun CH, Zhang H, Zhu WG, Wang J. Nucleic Acids Res. 46 689-703 (2018)
  4. Design of genetically encoded sensors to detect nucleosome ubiquitination in live cells. Dos Santos Passos C, Choi YS, Snow CD, Yao T, Cohen RE. J Cell Biol 220 e201911130 (2021)
  5. Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase. Anderson CJ, Baird MR, Hsu A, Barbour EH, Koyama Y, Borgnia MJ, McGinty RK. Cell Rep 26 1681-1690.e5 (2019)
  6. Abstract Abstracts. 7 (2018)


Reviews citing this publication (38)

  1. The control of DNA repair by the cell cycle. Hustedt N, Durocher D. Nat. Cell Biol. 19 1-9 (2016)
  2. The antitumorigenic roles of BRCA1-BARD1 in DNA repair and replication. Tarsounas M, Sung P. Nat Rev Mol Cell Biol 21 284-299 (2020)
  3. Histone ubiquitination in the DNA damage response. Uckelmann M, Sixma TK. DNA Repair (Amst.) 56 92-101 (2017)
  4. Reading chromatin signatures after DNA double-strand breaks. Wilson MD, Durocher D. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 372 (2017)
  5. Bromodomain proteins: repairing DNA damage within chromatin. Chiu LY, Gong F, Miller KM. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 372 (2017)
  6. Structural diversity of the nucleosome. Koyama M, Kurumizaka H. J. Biochem. 163 85-95 (2018)
  7. New factors in mammalian DNA repair-the chromatin connection. Raschellà G, Melino G, Malewicz M. Oncogene 36 4673-4681 (2017)
  8. RAP80, ubiquitin and SUMO in the DNA damage response. Lombardi PM, Matunis MJ, Wolberger C. J. Mol. Med. 95 799-807 (2017)
  9. Repair of DNA Double-Strand Breaks in Heterochromatin. Watts FZ. Biomolecules 6 (2016)
  10. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. J Mol Biol 429 3409-3429 (2017)
  11. Nucleosome structure and dynamics are coming of age. Zhou K, Gaullier G, Luger K. Nat. Struct. Mol. Biol. 26 3-13 (2019)
  12. Principles of Ubiquitin-Dependent Signaling. Oh E, Akopian D, Rape M. Annu. Rev. Cell Dev. Biol. 34 137-162 (2018)
  13. Nuclear cGAS: guard or prisoner? de Oliveira Mann CC, Hopfner KP. EMBO J 40 e108293 (2021)
  14. Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks. Fontana GA, Reinert JK, Thomä NH, Rass U. Microb Cell 5 327-343 (2018)
  15. The Histone Code of Senescence. Paluvai H, Di Giorgio E, Brancolini C. Cells 9 (2020)
  16. Biomolecular condensates at sites of DNA damage: More than just a phase. Spegg V, Altmeyer M. DNA Repair (Amst) 106 103179 (2021)
  17. Post-Translational Modifications of H2A Histone Variants and Their Role in Cancer. Corujo D, Buschbeck M. Cancers (Basel) 10 (2018)
  18. The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways. Chen Z, Tyler JK. Front Cell Dev Biol 10 909696 (2022)
  19. Total Chemical Synthesis of Modified Histones. Qi YK, Ai HS, Li YM, Yan B. Front Chem 6 19 (2018)
  20. Histone H2A variants: Diversifying chromatin to ensure genome integrity. Oberdoerffer P, Miller KM. Semin Cell Dev Biol 135 59-72 (2023)
  21. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Sanchez A, Lee D, Kim DI, Miller KM. Front Genet 12 747734 (2021)
  22. Ubiquitin and ubiquitin-like molecules in DNA double strand break repair. Yu J, Qin B, Lou Z. Cell Biosci 10 13 (2020)
  23. BRCA1/BARD1 is a nucleosome reader and writer. Witus SR, Zhao W, Brzovic PS, Klevit RE. Trends Biochem Sci 47 582-595 (2022)
  24. CENP-A nucleosome-a chromatin-embedded pedestal for the centromere: lessons learned from structural biology. Ali-Ahmad A, Sekulić N. Essays Biochem 64 205-221 (2020)
  25. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Karl LA, Peritore M, Galanti L, Pfander B. Front Genet 12 821543 (2021)
  26. DNA folds threaten genetic stability and can be leveraged for chemotherapy. Zell J, Rota Sperti F, Britton S, Monchaud D. RSC Chem Biol 2 47-76 (2021)
  27. Epigenetic signatures in cardiac fibrosis, special emphasis on DNA methylation and histone modification. Tao H, Song ZY, Ding XS, Yang JJ, Shi KH, Li J. Heart Fail Rev 23 789-799 (2018)
  28. From multi-omics approaches to personalized medicine in myocardial infarction. Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. Front Cardiovasc Med 10 1250340 (2023)
  29. Histone H2B Mutations in Cancer. Wan YCE, Chan KM. Biomedicines 9 694 (2021)
  30. It's all in the combination: decoding the epigenome for cancer research and diagnostics. Furth N, Shema E. Curr Opin Genet Dev 73 101899 (2022)
  31. Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. Zsidó BZ, Hetényi C. Int J Mol Sci 21 (2020)
  32. Molecular recognition of nucleosomes by binding partners. Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR. Curr Opin Struct Biol 56 164-170 (2019)
  33. Moving Mountains-The BRCA1 Promotion of DNA Resection. Densham RM, Morris JR. Front Mol Biosci 6 79 (2019)
  34. Nucleosome Remodeling by Fun30SMARCAD1 in the DNA Damage Response. Bantele SCS, Pfander B. Front Mol Biosci 6 78 (2019)
  35. Recognition of ubiquitinated nucleosomes. Morgan MT, Wolberger C. Curr. Opin. Struct. Biol. 42 75-82 (2017)
  36. Synthesis of ubiquitinated proteins for biochemical and functional analysis. Kriegesmann J, Brik A. Chem Sci 14 10025-10040 (2023)
  37. The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage. Tong ZB, Ai HS, Li JB. Front Cell Dev Biol 8 560098 (2020)
  38. Tools for Decoding Ubiquitin Signaling in DNA Repair. Foster B, Attwood M, Gibbs-Seymour I. Front Cell Dev Biol 9 760226 (2021)

Articles citing this publication (85)

  1. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, Schrock A, Campbell B, Shlien A, Chmielecki J, Huang F, He Y, Sun J, Tabori U, Kennedy M, Lieber DS, Roels S, White J, Otto GA, Ross JS, Garraway L, Miller VA, Stephens PJ, Frampton GM. Genome Med 9 34 (2017)
  2. Replication-Coupled Dilution of H4K20me2 Guides 53BP1 to Pre-replicative Chromatin. Pellegrino S, Michelena J, Teloni F, Imhof R, Altmeyer M. Cell Rep 19 1819-1831 (2017)
  3. Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. Poepsel S, Kasinath V, Nogales E. Nat. Struct. Mol. Biol. 25 154-162 (2018)
  4. ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair. Leung JW, Makharashvili N, Agarwal P, Chiu LY, Pourpre R, Cammarata MB, Cannon JR, Sherker A, Durocher D, Brodbelt JS, Paull TT, Miller KM. Genes Dev. 31 260-274 (2017)
  5. BRCA1 Haploinsufficiency Is Masked by RNF168-Mediated Chromatin Ubiquitylation. Zong D, Adam S, Wang Y, Sasanuma H, Callén E, Murga M, Day A, Kruhlak MJ, Wong N, Munro M, Ray Chaudhuri A, Karim B, Xia B, Takeda S, Johnson N, Durocher D, Nussenzweig A. Mol Cell 73 1267-1281.e7 (2019)
  6. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Skrajna A, Goldfarb D, Kedziora KM, Cousins EM, Grant GD, Spangler CJ, Barbour EH, Yan X, Hathaway NA, Brown NG, Cook JG, Major MB, McGinty RK. Nucleic Acids Res 48 9415-9432 (2020)
  7. Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break. Lou J, Priest DG, Solano A, Kerjouan A, Hinde E. Nat Commun 11 5776 (2020)
  8. Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18. Hu Q, Botuyan MV, Cui G, Zhao D, Mer G. Mol. Cell 66 473-487.e9 (2017)
  9. The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage. Kitevski-LeBlanc J, Fradet-Turcotte A, Kukic P, Wilson MD, Portella G, Yuwen T, Panier S, Duan S, Canny MD, van Ingen H, Arrowsmith CH, Rubinstein JL, Vendruscolo M, Durocher D, Kay LE. Elife 6 (2017)
  10. CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks. Rother MB, Pellegrino S, Smith R, Gatti M, Meisenberg C, Wiegant WW, Luijsterburg MS, Imhof R, Downs JA, Vertegaal ACO, Huet S, Altmeyer M, van Attikum H. Nat Commun 11 5775 (2020)
  11. Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends. Mattarocci S, Reinert JK, Bunker RD, Fontana GA, Shi T, Klein D, Cavadini S, Faty M, Shyian M, Hafner L, Shore D, Thomä NH, Rass U. Nat. Struct. Mol. Biol. 24 588-595 (2017)
  12. USP13 regulates the RAP80-BRCA1 complex dependent DNA damage response. Li Y, Luo K, Yin Y, Wu C, Deng M, Li L, Chen Y, Nowsheen S, Lou Z, Yuan J. Nat Commun 8 15752 (2017)
  13. Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures. Clouaire T, Rocher V, Lashgari A, Arnould C, Aguirrebengoa M, Biernacka A, Skrzypczak M, Aymard F, Fongang B, Dojer N, Iacovoni JS, Rowicka M, Ginalski K, Côté J, Legube G. Mol. Cell 72 250-262.e6 (2018)
  14. BRD4 Promotes DNA Repair and Mediates the Formation of TMPRSS2-ERG Gene Rearrangements in Prostate Cancer. Li X, Baek G, Ramanand SG, Sharp A, Gao Y, Yuan W, Welti J, Rodrigues DN, Dolling D, Figueiredo I, Sumanasuriya S, Crespo M, Aslam A, Li R, Yin Y, Mukherjee B, Kanchwala M, Hughes AM, Halsey WS, Chiang CM, Xing C, Raj GV, Burma S, de Bono J, Mani RS. Cell Rep 22 796-808 (2018)
  15. Chemical Synthesis of K34-Ubiquitylated H2B for Nucleosome Reconstitution and Single-Particle Cryo-Electron Microscopy Structural Analysis. Li J, He Q, Liu Y, Liu S, Tang S, Li C, Sun D, Li X, Zhou M, Zhu P, Bi G, Zhou Z, Zheng JS, Tian C. Chembiochem 18 176-180 (2017)
  16. Ubiquitin Phosphorylation at Thr12 Modulates the DNA Damage Response. Walser F, Mulder MPC, Bragantini B, Burger S, Gubser T, Gatti M, Botuyan MV, Villa A, Altmeyer M, Neri D, Ovaa H, Mer G, Penengo L. Mol Cell 80 423-436.e9 (2020)
  17. Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Gatchalian J, Wang X, Ikebe J, Cox KL, Tencer AH, Zhang Y, Burge NL, Di L, Gibson MD, Musselman CA, Poirier MG, Kono H, Hayes JJ, Kutateladze TG. Nat Commun 8 1489 (2017)
  18. Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Hu Q, Botuyan MV, Zhao D, Cui G, Mer E, Mer G. Nature 596 438-443 (2021)
  19. Letter Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome. Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J. Cell Res 29 330-333 (2019)
  20. PALB2 chromatin recruitment restores homologous recombination in BRCA1-deficient cells depleted of 53BP1. Belotserkovskaya R, Raga Gil E, Lawrence N, Butler R, Clifford G, Wilson MD, Jackson SP. Nat Commun 11 819 (2020)
  21. The ASCIZ-DYNLL1 axis promotes 53BP1-dependent non-homologous end joining and PARP inhibitor sensitivity. Becker JR, Cuella-Martin R, Barazas M, Liu R, Oliveira C, Oliver AW, Bilham K, Holt AB, Blackford AN, Heierhorst J, Jonkers J, Rottenberg S, Chapman JR. Nat Commun 9 5406 (2018)
  22. Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands. Weinberg DN, Rosenbaum P, Chen X, Barrows D, Horth C, Marunde MR, Popova IK, Gillespie ZB, Keogh MC, Lu C, Majewski J, Allis CD. Nat Genet 53 794-800 (2021)
  23. H4K20me2 distinguishes pre-replicative from post-replicative chromatin to appropriately direct DNA repair pathway choice by 53BP1-RIF1-MAD2L2. Simonetta M, de Krijger I, Serrat J, Moatti N, Fortunato D, Hoekman L, Bleijerveld OB, Altelaar AFM, Jacobs JJL. Cell Cycle 17 124-136 (2018)
  24. Histone Variant H2A.J Marks Persistent DNA Damage and Triggers the Secretory Phenotype in Radiation-Induced Senescence. Isermann A, Mann C, Rübe CE. Int J Mol Sci 21 E9130 (2020)
  25. Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein. Botuyan MV, Cui G, Drané P, Oliveira C, Detappe A, Brault ME, Parnandi N, Chaubey S, Thompson JR, Bragantini B, Zhao D, Chapman JR, Chowdhury D, Mer G. Nat. Struct. Mol. Biol. 25 591-600 (2018)
  26. Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR. Wang J, Yuan Z, Cui Y, Xie R, Yang G, Kassab MA, Wang M, Ma Y, Wu C, Yu X, Liu X. Nat Commun 9 2689 (2018)
  27. A Screen for Epstein-Barr Virus Proteins That Inhibit the DNA Damage Response Reveals a Novel Histone Binding Protein. Ho TH, Sitz J, Shen Q, Leblanc-Lacroix A, Campos EI, Borozan I, Marcon E, Greenblatt J, Fradet-Turcotte A, Jin DY, Frappier L. J. Virol. 92 (2018)
  28. Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1. Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB. Proc. Natl. Acad. Sci. U.S.A. 115 8775-8780 (2018)
  29. Cryo-EM of nucleosome core particle interactions in trans. Bilokapic S, Strauss M, Halic M. Sci Rep 8 7046 (2018)
  30. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nakamura K, Saredi G, Becker JR, Foster BM, Nguyen NV, Beyer TE, Cesa LC, Faull PA, Lukauskas S, Frimurer T, Chapman JR, Bartke T, Groth A. Nat. Cell Biol. 21 311-318 (2019)
  31. RNF169 limits 53BP1 deposition at DSBs to stimulate single-strand annealing repair. An L, Dong C, Li J, Chen J, Yuan J, Huang J, Chan KM, Yu CH, Huen MSY. Proc. Natl. Acad. Sci. U.S.A. 115 E8286-E8295 (2018)
  32. Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing. Zhang Z, Jones AE, Wu W, Kim J, Kang Y, Bi X, Gu Y, Popov IK, Renfrow MB, Vassylyeva MN, Vassylyev DG, Giles KE, Chen D, Kumar A, Fan Y, Tong Y, Liu CF, An W, Chang C, Luo J, Chow LT, Wang H. Proc. Natl. Acad. Sci. U.S.A. 114 E7949-E7958 (2017)
  33. The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions. Murawska M, Schauer T, Matsuda A, Wilson MD, Pysik T, Wojcik F, Muir TW, Hiraoka Y, Straub T, Ladurner AG. Mol Cell 77 501-513.e7 (2020)
  34. The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation. Xu X, Ni K, He Y, Ren J, Sun C, Liu Y, Aladjem MI, Burkett S, Finney R, Ding X, Sharan SK, Muegge K. Nat Commun 12 3520 (2021)
  35. Ubiquitin-specific protease 7 sustains DNA damage response and promotes cervical carcinogenesis. Su D, Ma S, Shan L, Wang Y, Wang Y, Cao C, Liu B, Yang C, Wang L, Tian S, Ding X, Liu X, Yu N, Song N, Liu L, Yang S, Zhang Q, Yang F, Zhang K, Shi L. J. Clin. Invest. 128 4280-4296 (2018)
  36. A cell cycle-independent mode of the Rad9-Dpb11 interaction is induced by DNA damage. di Cicco G, Bantele SCS, Reusswig KU, Pfander B. Sci Rep 7 11650 (2017)
  37. Letter Chemically synthesized histone H2A Lys13 di-ubiquitination promotes binding of 53BP1 to nucleosomes. Li JB, Qi YK, He QQ, Ai HS, Liu SL, Wang JX, Zheng JS, Liu L, Tian C. Cell Res. 28 257-260 (2018)
  38. Crosstalk between Lys63- and Lys11-polyubiquitin signaling at DNA damage sites is driven by Cezanne. Wu X, Liu S, Sagum C, Chen J, Singh R, Chaturvedi A, Horton JR, Kashyap TR, Fushman D, Cheng X, Bedford MT, Wang B. Genes Dev 33 1702-1717 (2019)
  39. Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence. Takizawa Y, Tanaka H, Machida S, Koyama M, Maehara K, Ohkawa Y, Wade PA, Wolf M, Kurumizaka H. Open Biol 8 (2018)
  40. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S. Nat Commun 9 170 (2018)
  41. Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome. Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S. Elife 10 e71420 (2021)
  42. The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Cai S, Böck D, Pilhofer M, Gan L. Mol. Biol. Cell 29 2450-2457 (2018)
  43. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Korolev N, Lyubartsev AP, Nordenskiöld L. Sci Rep 8 1543 (2018)
  44. An E2-guided E3 Screen Identifies the RNF17-UBE2U Pair as Regulator of the Radiosensitivity, Immunodeficiency, Dysmorphic Features, and Learning Difficulties (RIDDLE) Syndrome Protein RNF168. Guo Y, An L, Ng HM, Sy SM, Huen MS. J. Biol. Chem. 292 967-978 (2017)
  45. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ. Bayley R, Borel V, Moss RJ, Sweatman E, Ruis P, Ormrod A, Goula A, Mottram RMA, Stanage T, Hewitt G, Saponaro M, Stewart GS, Boulton SJ, Higgs MR. Mol Cell 82 1924-1939.e10 (2022)
  46. Lamin B1 sequesters 53BP1 to control its recruitment to DNA damage. Etourneaud L, Moussa A, Rass E, Genet D, Willaume S, Chabance-Okumura C, Wanschoor P, Picotto J, Thézé B, Dépagne J, Veaute X, Dizet E, Busso D, Barascu A, Irbah L, Kortulewski T, Campalans A, Le Chalony C, Zinn-Justin S, Scully R, Pennarun G, Bertrand P. Sci Adv 7 eabb3799 (2021)
  47. The convergent chemical synthesis of histone H3 protein for site-specific acetylation at Lys56 and ubiquitination at Lys122. Qi YK, He QQ, Ai HS, Guo J, Li JB. Chem. Commun. (Camb.) 53 4148-4151 (2017)
  48. An AlphaFold2 map of the 53BP1 pathway identifies a direct SHLD3-RIF1 interaction critical for shieldin activity. Sifri C, Hoeg L, Durocher D, Setiaputra D. EMBO Rep 24 e56834 (2023)
  49. Dietary restriction delays the secretion of senescence associated secretory phenotype by reducing DNA damage response in the process of renal aging. Wang W, Cai G, Chen X. Exp. Gerontol. 107 4-10 (2018)
  50. Ectopic RNF168 expression promotes break-induced replication-like DNA synthesis at stalled replication forks. Krais JJ, Johnson N. Nucleic Acids Res 48 4298-4308 (2020)
  51. LC8/DYNLL1 is a 53BP1 effector and regulates checkpoint activation. West KL, Kelliher JL, Xu Z, An L, Reed MR, Eoff RL, Wang J, Huen MSY, Leung JWC. Nucleic Acids Res. 47 6236-6249 (2019)
  52. Lysine Methyltransferase Inhibitors Impair H4K20me2 and 53BP1 Foci in Response to DNA Damage in Sarcomas, a Synthetic Lethality Strategy. Campillo-Marcos I, Monte-Serrano E, Navarro-Carrasco E, García-González R, Lazo PA. Front Cell Dev Biol 9 715126 (2021)
  53. The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair. Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM. Sci Rep 9 6539 (2019)
  54. 53BP1 Supports Immunoglobulin Class Switch Recombination Independently of Its DNA Double-Strand Break End Protection Function. Sundaravinayagam D, Rahjouei A, Andreani M, Tupiņa D, Balasubramanian S, Saha T, Delgado-Benito V, Coralluzzo V, Daumke O, Di Virgilio M. Cell Rep 28 1389-1399.e6 (2019)
  55. A role of the 53BP1 protein in genome protection: structural and functional characteristics of 53BP1-dependent DNA repair. Bártová E, Legartová S, Dundr M, Suchánková J. Aging (Albany NY) 11 2488-2511 (2019)
  56. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. Nat Commun 14 6091 (2023)
  57. BRCA1-BARD1 combines multiple chromatin recognition modules to bridge nascent nucleosomes. Burdett H, Foglizzo M, Musgrove LJ, Kumar D, Clifford G, Campbell LJ, Heath GR, Zeqiraj E, Wilson MD. Nucleic Acids Res 51 11080-11103 (2023)
  58. BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1. Witus SR, Burrell AL, Farrell DP, Kang J, Wang M, Hansen JM, Pravat A, Tuttle LM, Stewart MD, Brzovic PS, Chatterjee C, Zhao W, DiMaio F, Kollman JM, Klevit RE. Nat Struct Mol Biol (2021)
  59. Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS. Papanastasiou M, Mullahoo J, DeRuff KC, Bajrami B, Karageorgos I, Johnston SE, Peckner R, Myers SA, Carr SA, Jaffe JD. Mol. Cell Proteomics 18 2089-2098 (2019)
  60. Clinical and Biological Manifestation of RNF168 Deficiency in Two Polish Siblings. Pietrucha B, Heropolitańska-Pliszka E, Geffers R, Enßen J, Wieland B, Bogdanova NV, Dörk T. Front Immunol 8 1683 (2017)
  61. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Nat Commun 10 5540 (2019)
  62. Examination of the Deubiquitylation Site Selectivity of USP51 by Using Chemically Synthesized Ubiquitylated Histones. Ai H, Guo Y, Sun D, Liu S, Qi Y, Guo J, Qu Q, Gong Q, Zhao S, Li J, Liu L. Chembiochem 20 221-229 (2019)
  63. Histone H2A variants alpha1-extension helix directs RNF168-mediated ubiquitination. Kelliher JL, West KL, Gong Q, Leung JWC. Nat Commun 11 2462 (2020)
  64. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. Wang ZA, Whedon SD, Wu M, Wang S, Brown EA, Anmangandla A, Regan L, Lee K, Du J, Hong JY, Fairall L, Kay T, Lin H, Zhao Y, Schwabe JWR, Cole PA. J Am Chem Soc 144 3360-3364 (2022)
  65. Histone divergence in trypanosomes results in unique alterations to nucleosome structure. Deák G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson JA, Tuijtel MW, Webb S, Wilson MD. Nucleic Acids Res 51 7882-7899 (2023)
  66. Human papillomavirus E7 oncoprotein targets RNF168 to hijack the host DNA damage response. Sitz J, Blanchet SA, Gameiro SF, Biquand E, Morgan TM, Galloy M, Dessapt J, Lavoie EG, Blondeau A, Smith BC, Mymryk JS, Moody CA, Fradet-Turcotte A. Proc. Natl. Acad. Sci. U.S.A. 116 19552-19562 (2019)
  67. Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study. Oleinikov PD, Fedulova AS, Armeev GA, Motorin NA, Singh-Palchevskaia L, Sivkina AL, Feskin PG, Glukhov GS, Afonin DA, Komarova GA, Kirpichnikov MP, Studitsky VM, Feofanov AV, Shaytan AK. Int J Mol Sci 24 15194 (2023)
  68. Laser Microirradiation and Real-time Recruitment Assays Using an Engineered Biosensor. Passos CDS, Cohen RE, Yao T. Bio Protoc 12 e4337 (2022)
  69. MDC1 PST-repeat region promotes histone H2AX-independent chromatin association and DNA damage tolerance. Salguero I, Belotserkovskaya R, Coates J, Sczaniecka-Clift M, Demir M, Jhujh S, Wilson MD, Jackson SP. Nat Commun 10 5191 (2019)
  70. New perspectives on epigenetic modifications and PARP inhibitor resistance in HR-deficient cancers. Bayley R, Sweatman E, Higgs MR. Cancer Drug Resist 6 35-44 (2023)
  71. Nucleosomes and their complexes in the cryoEM era: Trends and limitations. Armeev GA, Gribkova AK, Shaytan AK. Front Mol Biosci 9 1070489 (2022)
  72. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Cell 179 470-484.e21 (2019)
  73. Phosphorylation of TIP60 Suppresses 53BP1 Localization at DNA Damage Sites. Li ML, Jiang Q, Bhanu NV, Wu J, Li W, Garcia BA, Greenberg RA. Mol. Cell. Biol. 39 (2019)
  74. RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity. Feng S, Ma S, Li K, Gao S, Ning S, Shang J, Guo R, Chen Y, Blumenfeld B, Simon I, Li Q, Guo R, Xu D. Nat Commun 13 957 (2022)
  75. Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer. Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE, Nans A, Rueda DS, Cherepanov P, Costa A. Nat Commun 10 4189 (2019)
  76. Semisynthesis of ubiquitinated histone H2B with a native or nonhydrolyzable linkage. Morgan M, Jbara M, Brik A, Wolberger C. Methods Enzymol 618 1-27 (2019)
  77. Site-specific targeting of a light activated dCas9-KillerRed fusion protein generates transient, localized regions of oxidative DNA damage. House NCM, Parasuram R, Layer JV, Price BD. PLoS One 15 e0237759 (2020)
  78. Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1. Thomas JF, Valencia-Sánchez MI, Tamburri S, Gloor SL, Rustichelli S, Godínez-López V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ. Sci Adv 9 eadg9832 (2023)
  79. Structural basis of specific H2A K13/K15 ubiquitination by RNF168. Horn V, Uckelmann M, Zhang H, Eerland J, Aarsman I, le Paige UB, Davidovich C, Sixma TK, van Ingen H. Nat Commun 10 1751 (2019)
  80. News Switching 53BP1 on and off via Tudors. Zhang Y, Kutateladze TG. Nat. Struct. Mol. Biol. 25 646-647 (2018)
  81. Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes. Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L. Nat Struct Mol Biol (2024)
  82. Systematic analysis of the molecular and biophysical properties of key DNA damage response factors. Heyza JR, Mikhova M, Bahl A, Broadbent DG, Schmidt JC. Elife 12 e87086 (2023)
  83. TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks. Ma J, Zhou Y, Pan P, Yu H, Wang Z, Li LL, Wang B, Yan Y, Pan Y, Ye Q, Liu T, Feng X, Xu S, Wang K, Wang X, Jian Y, Ma B, Fan Y, Gao Y, Huang H, Li L. Nat Commun 14 1810 (2023)
  84. The dCypher Approach to Interrogate Chromatin Reader Activity Against Posttranslational Modification-Defined Histone Peptides and Nucleosomes. Marunde MR, Popova IK, Weinzapfel EN, Keogh MC. Methods Mol Biol 2458 231-255 (2022)
  85. Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage. Kochan JA, van den Belt M, von der Lippe J, Desclos ECB, Steurer B, Hoebe RA, Scutigliani EM, Verhoeven J, Stap J, Bosch R, Rijpkema M, van Oven C, van Veen HA, Stellingwerf I, Vriend LEM, Marteijn JA, Aten JA, Krawczyk PM. Nucleic Acids Res. 47 e100 (2019)


Quick links