Cited by 3Genomics and Chromatin DynamicsProtein Structure and DynamicsNuclear Structure and Function

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Disordered regions and folded modules in CAF-1 promote histone deposition in Schizosaccharomyces pombe

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Ouasti, Fouad, Audin, Maxime, Fréon, Karine, Quivy, Jean-Pierre, Tachekort, Mehdi, Cesard, Elizabeth, Thureau, Aurélien, Ropars, Virginie, Fernández Varela, Paloma, Moal, Gwenaelle, Soumana Adamou, Ibrahim, Uryga, Aleksandra, Legrand, Pierre, Andreani, Jessica, Guerois, Raphaël, Almouzni, Geneviève, Lambert, Sarah, Ochsenbein, Francoise·2024·eLife

Published version of a preprint

Abstract

Genome and epigenome integrity in eukaryotes depends on the proper coupling of histone deposition with DNA synthesis. This process relies on the evolutionary conserved histone chaperone CAF-1 for which the links between structure and functions are still a puzzle. While studies of the Saccharomyces cerevisiae CAF-1 complex enabled to propose a model for the histone deposition mechanism, we still lack a framework to demonstrate its generality and in particular, how its interaction with the polymerase accessory factor PCNA is operating. Here, we reconstituted a complete Sp CAF-1 from fission yeast. We characterized its dynamic structure using NMR, SAXS and molecular modeling together with in vitro and in vivo functional studies on rationally designed interaction mutants. Importantly, we identify the unfolded nature of the acidic domain which folds up when binding to histones. We also show how the long KER helix mediates DNA binding and stimulates Sp CAF-1 association with PCNA. Our study highlights how the organization of CAF-1 comprising both disordered regions and folded modules enables the dynamics of multiple interactions to promote synthesis-coupled histone deposition essential for its DNA replication, heterochromatin maintenance, and genome stability functions.

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Research works printed but not linked: 65

  1. Anderson, 2010, Co-expression as a convenient method for the production and purification of core histones in bacteria, Protein Expression and Purification, 72, 194, 10.1016/j.pep.2010.03.013 · DOI
  2. Ayoub, 2022, Biochemical and structural insights into the winged helix domain of p150, the largest subunit of the chromatin assembly factor 1, International Journal of Molecular Sciences, 23, 10.3390/ijms23042160 · DOI
  3. Bedina, 2013, Intrinsically disoredered proteins in replication process, Trends in Biochemical Sciences, 37, 10.5772/3433 · DOI
  4. Berger, 2004, Baculovirus expression system for heterologous multiprotein complexes, Nature Biotechnology, 22, 1583, 10.1038/nbt1036 · DOI
  5. Brookes, 2016, US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data, Journal of Applied Crystallography, 49, 1827, 10.1107/S1600576716011201 · DOI
  6. Delaglio, 1995, NMRPipe: a multidimensional spectral processing system based on UNIX pipes, Journal of Biomolecular NMR, 6, 277, 10.1007/BF00197809 · DOI
  7. Dohke, 2008, Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin, Genes to Cells, 13, 1027, 10.1111/j.1365-2443.2008.01225.x · DOI
  8. Evans, 2022, Protein Complex Prediction with Alphafold-Multimer, 10.1101/2021.10.04.463034 · DOI · Paper page
  9. Gopinathan Nair, 2022, Unorthodox PCNA Binding by chromatin assembly factor 1, International Journal of Molecular Sciences, 23, 10.3390/ijms231911099 · DOI
  10. Gurard-Levin, 2014, Histone chaperones: assisting histone traffic and nucleosome dynamics, Annual Review of Biochemistry, 83, 487, 10.1146/annurev-biochem-060713-035536 · DOI
  11. Hardy, 2019, Histone deposition promotes recombination-dependent replication at arrested forks, PLOS Genetics, 15, 10.1371/journal.pgen.1008441 · DOI
  12. Huang, 2015, A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks, Nature Structural & Molecular Biology, 22, 618, 10.1038/nsmb.3055 · DOI
  13. Janke, 2018, Pivotal roles of PCNA loading and unloading in heterochromatin function, PNAS, 115, E2030, 10.1073/pnas.1721573115 · DOI
  14. Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Molecular Biology and Evolution, 30, 772, 10.1093/molbev/mst010 · DOI · Paper page
  15. Kaufman, 1995, The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication, Cell, 81, 1105, 10.1016/s0092-8674(05)80015-7 · DOI
  16. Kaufman, 1997, Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I, Genes & Development, 11, 345, 10.1101/gad.11.3.345 · DOI
  17. Kaufman, 1998, Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I, Molecular and Cellular Biology, 18, 4793, 10.1128/MCB.18.8.4793 · DOI
  18. Krawitz, 2002, Chromatin assembly factor I mutants defective for PCNA binding require Asf1/Hir proteins for silencing, Molecular and Cellular Biology, 22, 614, 10.1128/MCB.22.2.614-625.2002 · DOI
  19. Leman, 2020, Macromolecular modeling and design in rosetta: recent methods and frameworks, Nature Methods, 17, 665, 10.1038/s41592-020-0848-2 · DOI · Paper page
  20. Liu, 2012, CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA, Nucleic Acids Research, 40, 11229, 10.1093/nar/gks906 · DOI
  21. Liu, 2016, The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones, eLife, 5, 10.7554/eLife.18023 · DOI
  22. Loyola, 2004, Histone chaperones, a supporting role in the limelight, Biochimica et Biophysica Acta, 1677, 3, 10.1016/j.bbaexp.2003.09.012 · DOI
  23. Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 a resolution, Nature, 389, 251, 10.1038/38444 · DOI · Paper page
  24. Ma, 2021, Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies, The EMBO Journal, 40, 10.15252/embj.2020106632 · DOI
  25. Manalastas-Cantos, 2021, ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis, Journal of Applied Crystallography, 54, 343, 10.1107/S1600576720013412 · DOI
  26. Martini, 1998, Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells, The Journal of Cell Biology, 143, 563, 10.1083/jcb.143.3.563 · DOI
  27. Mattiroli, 2017, The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1, Scientific Reports, 7, 10.1038/srep46274 · DOI
  28. Mattiroli, 2017, DNA-mediated association of two histone-bound complexes of yeast chromatin assembly factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication, eLife, 6, 10.7554/eLife.22799 · DOI
  29. Mejlvang, 2014, New histone supply regulates replication fork speed and PCNA unloading, The Journal of Cell Biology, 204, 29, 10.1083/jcb.201305017 · DOI
  30. Miele, 2022, The Xer activation factor of TLCΦ expands the possibilities for Xer recombination, Nucleic Acids Research, 50, 6368, 10.1093/nar/gkac429 · DOI
  31. Mirdita, 2022, Colabfold: making protein folding accessible to all, Nature Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  32. Moggs, 2000, A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage, Molecular and Cellular Biology, 20, 1206, 10.1128/MCB.20.4.1206-1218.2000 · DOI
  33. Pietrobon, 2014, The chromatin assembly factor 1 promotes Rad51-dependent template switches at replication forks by counteracting D-loop disassembly by the RecQ-type helicase Rqh1, PLOS Biology, 12, 10.1371/journal.pbio.1001968 · DOI
  34. Rambo, 2013, Accurate assessment of mass, models and resolution by small-angle scattering, Nature, 496, 477, 10.1038/nature12070 · DOI · Paper page
  35. Ray-Gallet, 2004, DNA synthesis-dependent and -independent chromatin assembly pathways in Xenopus egg extracts, Methods in Enzymology, 375, 117, 10.1016/s0076-6879(03)75008-3 · DOI
  36. Ray-Gallet, 2011, Dynamics of histone H3 deposition in vivo reveal a nucleosome gap-filling mechanism for H3.3 to maintain chromatin integrity, Molecular Cell, 44, 928, 10.1016/j.molcel.2011.12.006 · DOI
  37. Ray-Gallet, 2022, H3-H4 histone chaperones and cancer, Current Opinion in Genetics & Development, 73, 10.1016/j.gde.2022.101900 · DOI
  38. Richet, 2015, Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork, Nucleic Acids Research, 43, 1905, 10.1093/nar/gkv021 · DOI
  39. Ridgway, 2000, CAF-1 and the inheritance of chromatin states: at the crossroads of DNA replication and repair, Journal of Cell Science, 113 ( Pt 15), 2647, 10.1242/jcs.113.15.2647 · DOI
  40. Rolef Ben-Shahar, 2009, Two fundamentally distinct PCNA interaction peptides contribute to chromatin assembly factor 1 function, Molecular and Cellular Biology, 29, 6353, 10.1128/MCB.01051-09 · DOI
  41. Rosas, 2023, A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function, eLife, 12, 10.7554/eLife.83538 · DOI
  42. Rouillon, 2023, CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands, Nucleic Acids Research, 51, 3770, 10.1093/nar/gkad171 · DOI
  43. Rudenko O, Thureau A, Perez J. 2019. Evolutionary refinement of the 3D structure of multi-domain protein complexes from small angle X-ray scattering data. Proceedings of the 2019 Genetic and Evolutionary Computation Conference Companion (Geccco’19 Companion.
  44. Sauer, 2017, Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast chromatin assembly factor 1, eLife, 6, 10.7554/eLife.23474 · DOI
  45. Sauer, 2018, Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1, Nucleic Acids Research, 46, 9907, 10.1093/nar/gky823 · DOI
  46. Shen, 2007, Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology, Journal of Biomolecular NMR, 38, 289, 10.1007/s10858-007-9166-6 · DOI
  47. Shen, 2008, Consistent blind protein structure generation from NMR chemical shift data, PNAS, 105, 4685, 10.1073/pnas.0800256105 · DOI · Paper page
  48. Shibahara, 1999, Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin, Cell, 96, 575, 10.1016/s0092-8674(00)80661-3 · DOI
  49. Smith, 1989, Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro, Cell, 58, 15, 10.1016/0092-8674(89)90398-x · DOI
  50. Steinegger, 2017, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nature Biotechnology, 35, 1026, 10.1038/nbt.3988 · DOI · Paper page
  51. Steinegger, 2019, HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinformatics, 20, 10.1186/s12859-019-3019-7 · DOI · Paper page
  52. Sultana, 2021, Insights into the roles of histone chaperones in nucleosome assembly and disassembly in virus infection, Virus Research, 297, 10.1016/j.virusres.2021.198395 · DOI
  53. Tamiola, 2010, Sequence-specific random coil chemical shifts of intrinsically disordered proteins, Journal of the American Chemical Society, 132, 18000, 10.1021/ja105656t · DOI
  54. Thakar, 2020, Ubiquitinated-PCNA protects replication forks from DNA2-mediated degradation by regulating okazaki fragment maturation and chromatin assembly, Nature Communications, 11, 10.1038/s41467-020-16096-w · DOI
  55. Thureau, 2021, BioSAXS on the SWING beamline at synchrotron SOLEIL, Journal of Applied Crystallography, 54, 1698, 10.1107/S1600576721008736 · DOI
  56. Tso, 2018, Using two-site binding models to analyze microscale thermophoresis data, Analytical Biochemistry, 540–541, 64, 10.1016/j.ab.2017.10.013 · DOI
  57. UniProt, 2021, Uniprot: the universal protein knowledgebase in 2021, Nucleic Acids Research, 49, D480, 10.1093/nar/gkaa1100 · DOI · Paper page
  58. Wishart, 1995, (1)H, (13)C and (15)N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects, Journal of Biomolecular NMR, 5, 10.1007/BF00211764 · DOI
  59. Wishart, 1995, 1H, 13C and 15N chemical shift referencing in biomolecular NMR, Journal of Biomolecular NMR, 6, 135, 10.1007/BF00211777 · DOI
  60. Yi, 2020, New insights into the role of histone changes in aging, International Journal of Molecular Sciences, 21, 10.3390/ijms21218241 · DOI
  61. Zhang, 2000, PCNA connects DNA replication to epigenetic inheritance in yeast, Nature, 408, 221, 10.1038/35041601 · DOI
  62. Zhang, 2016, A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks, Nucleic Acids Research, 44, 5083, 10.1093/nar/gkw106 · DOI
  63. Guerois R, Ochsenbein F. 2023. Model of the complex between the histone chaperones Pcf1 (ortholog of CAF1 subunit A in human) and Pcf2 (ortholog of CAF1 subunit B in human) in S. pombe. ModelArchive. · DOI
  64. Guerois R, Ochsenbein F. 2023. Model of the complex between the histone chaperones Pcf1 (ortholog of CAF1 subunit A in human) and Pcf3 (ortholog of CAF1 subunit C in human) in S. pombe. ModelArchive. · DOI
  65. Guerois R, Ochsenbein F. 2023. Model of the complex between the histone chaperones Pcf1 (ortholog of CAF1 subunit A in human) and histones H3 and H4 in S. pombe. ModelArchive. · DOI

Metadata

Authors
Ouasti, F., Audin, M., Fréon, K., Quivy, J.-P., Tachekort, M., Cesard, E., Thureau, A., Ropars, V., Fernández Varela, P., Moal, G., Soumana Adamou, I., Uryga, A., Legrand, P., Andreani, J., Guerois, R., Almouzni, G., Lambert, S., & Ochsenbein, F.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Synchrotron SOLEIL (FR)
  • Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Institute Joliot
  • Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Université Paris-Saclay, Equipe labellisée Ligue contre le Cancer
Venue
eLife
Published
2024-02-20
Volume
12
ISSN
2050-084X (ISSN-L)
OpenAlex
W4391981040
Cited by
3
References
1
Citations by year
2025: 2 · 2024: 1
FWCI
0.41
Type
journal article
Language
en
Open access
Locations
eLife (publishedVersion, cc-by)
Funders
  • Institut National Du Cancer (2016-1-PL BIO-03-CEA1, 2016-1-PLBIO-03-ICR-1)
  • Agence Nationale de la Recherche (ANR-16-CE11-0028, ANR-20-CE18-0038)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
histone deposition, Schizosaccharomyces pombe, intrinsically disordered regions, protein structure-function relationship, PCNA, DNA replication, heterochromatin maintenance, genome stability, protein complex reconstitution

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