CoChat
Sign Up
PreprintCited by 58Microtubule and mitosis dynamicsGenomics and Chromatin DynamicsNuclear Structure and Function

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere

Open access
Dendooven, Tom, Zhang, Ziguo, Yang, Jing, McLaughlin, Stephen H., Schwab, Johannes, Scheres, Sjors H.W., Yatskevich, Stanislau, Barford, David·2022·Science Advances
DOI 10.1101/2022.12.12.520091PMC PMC10381965

Preprint — published as 10.1126/sciadv.adg7480 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Summary: The point centromere of budding yeast specifies assembly of the large multi-subunit kinetochore complex. By direct attachment to the mitotic spindle, kinetochores couple the forces of microtubule dynamics to power chromatid segregation at mitosis. Kinetochores share a conserved architecture comprising the centromere-associated inner kinetochore CCAN (constitutive centromere-associated network) complex and the microtubule-binding outer kinetochore KMN network. The budding yeast inner kinetochore additionally includes the centromere-binding CBF1 and CBF3 complexes. Here, we reconstituted the complete yeast inner kinetochore complex assembled onto the centromere-specific CENP-A nucleosome (CENP-A Nuc ) and determined its structure using cryo-EM. This revealed a central CENP-A Nuc , wrapped by only one turn of DNA, and harboring extensively unwrapped DNA ends. These free DNA duplexes function as binding sites for two CCAN protomers, one of which entraps DNA topologically and is positioned precisely on the centromere by the sequence-specific DNA-binding complex CBF1. The CCAN protomers are connected through CBF3 to form an arch-like configuration, binding 150 bp of DNA. We also define a structural model for a CENP-A Nuc -pathway to the outer kinetochore involving only CENP-QU. This study presents a framework for understanding the basis of complete inner kinetochore assembly onto a point centromere, and how it organizes the outer kinetochore for robust chromosome attachment to the mitotic spindle.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2022.12.12.520091

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 108

  1. 10.1107/S0907444912001308 · DOI · Paper page
  2. 10.1101/gad.1865909 · DOI
  3. Anedchenko, E.A. , Samel-Pommerencke, A. , Tran Nguyen, T.M. , Shahnejat-Bushehri, S. , Popsel, J. , Lauster, D. , Herrmann, A. , Rappsilber, J. , Cuomo, A. , Bonaldi, T. , et al. (2019). The kinetochore module Okp1(CENP-Q)/Ame1(CENP-U) is a reader for N-terminal modifications on the centromeric histone Cse4(CENP-A). The EMBO journal 38. · DOI
  4. 2013, The budding yeast point centromere associates with two Cse4 molecules during mitosis, Current biology : CB, 23, 770, 10.1016/j.cub.2013.03.042 · DOI
  5. 10.1128/MCB.10.6.2458 · DOI
  6. 10.1534/genetics.105.046458 · DOI
  7. 10.1093/nar/27.6.1444 · DOI
  8. 2019, Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs, Nat Methods, 16, 1153, 10.1038/s41592-019-0575-8 · DOI
  9. 10.1016/0092-8674(82)90147-7 · DOI
  10. 2021, The Proteomic Landscape of Centromeric Chromatin Reveals an Essential Role for the Ctf19(CCAN) Complex in Meiotic Kinetochore Assembly, Current biology : CB, 31, 283, 10.1016/j.cub.2020.10.025 · DOI
  11. 10.1083/jcb.123.2.387 · DOI
  12. 10.1016/0092-8674(90)90525-J · DOI
  13. 10.1016/j.molcel.2007.05.013 · DOI
  14. 10.1016/j.molcel.2009.07.022 · DOI
  15. 10.1083/jcb.201001013 · DOI
  16. 10.1038/ncb1899 · DOI
  17. 10.1016/S0092-8674(02)00973-X · DOI
  18. 10.1038/s41592-021-01220-5 · DOI
  19. 10.1128/MCB.20.18.7037-7048.2000 · DOI
  20. 10.1073/pnas.1106389108 · DOI
  21. Cieslinski, K. , Wu, Y.-L. , Nechyporenko, L. , Hörner, S.J. , Conti, D. Skruzny , and Reis, J. (2021). Nanoscale structural organization and stoichiometry of the budding 1 yeast kinetochore. BioRxiv. · DOI
  22. 10.1038/287504a0 · DOI
  23. 10.1038/305023a0 · DOI
  24. 10.1091/mbc.E08-03-0297 · DOI
  25. 10.1073/pnas.1104978108 · DOI
  26. 10.1128/MCB.9.8.3342 · DOI
  27. 1987, Mutational analysis of meiotic and mitotic centromere function in Saccharomyces cerevisiae, Genetics, 117, 203, 10.1093/genetics/117.2.203 · DOI
  28. 10.1101/gad.1144403 · DOI
  29. 2011, Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes, Nature communications, 2, 313, 10.1038/ncomms1320 · DOI
  30. 10.1083/jcb.201703152 · DOI
  31. 1993, Identification of essential components of the S, cerevisiae kinetochore. Cell, 73, 761
  32. 10.1093/nar/20.16.4229 · DOI
  33. 10.1007/BF00328227 · DOI
  34. 10.1107/S0907444910007493 · DOI · Paper page
  35. Evans, R. , O’Neill, M. , Pritzel, A. , Antropova, N. , Senior, A.W. , Green, T. , Zidek, A. , Bates, R. , Blackwell, S. , Yim, J. , et al. (2022). Protein complex prediction with AlphaFold-Multimer. BioRxiv. · DOI · Paper page
  36. 10.1038/363038a0 · DOI
  37. Fischbock-Halwachs, J. , Singh, S. , Potocnjak, M. , Hagemann, G. , Solis-Mezarino, V. , Woike, S. , Ghodgaonkar-Steger, M. , Weissmann, F. , Gallego, L.D. , Rojas, J. , et al. (2019). The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore. eLife 8. · DOI
  38. 10.1016/0092-8674(82)90108-8 · DOI
  39. 1993, Point mutations that separate the role of Saccharomyces cerevisiae centromere binding factor 1 in chromosome segregation from its role in transcriptional activation, Genetics, 135, 287, 10.1093/genetics/135.2.287 · DOI
  40. 1989, Chromatin digestion with restriction endonucleases reveals 150-160 bp of protected DNA in the centromere of chromosome XIV in Saccharomyces cerevisiae, Molecular & general genetics : MGG, 219, 153, 10.1007/BF00261171 · DOI
  41. 10.1073/pnas.0706985104 · DOI
  42. 10.1128/MCB.7.1.68 · DOI
  43. 1989, Mutations in CEN3 cause aberrant chromosome segregation during meiosis in Saccharomyces cerevisiae, Genetics, 121, 477, 10.1093/genetics/121.3.477 · DOI
  44. 10.1002/PRO.3235 · DOI · Paper page
  45. 10.1083/jcb.121.3.503 · DOI
  46. 10.1371/journal.pgen.1002190 · DOI
  47. 2021, Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation, Nature communications, 12, 1763, 10.1038/s41467-021-21985-9 · DOI
  48. Hagemann, G. , Solis-Mezarino, V. , Singh, S. , Potocnjak, M. , Kumar, C. , and Herzog, F. (2022). Quantitative crosslinking and mass spectrometry determine binding interfaces and affinities mediating kinetochore stabilization. bioRxiv 20211228474328. · DOI
  49. Hamilton, G.E. , Helgeson, L.A. , Noland, C.L. , Asbury, C.L. , Dimitrova, Y.N. , and Davis, T.N. (2020). Reconstitution reveals two paths of force transmission through the kinetochore. eLife 9. · DOI
  50. 1988, Mutational analysis of centromere DNA from chromosome VI of Saccharomyces cerevisiae, Molecular and cellular biology, 8, 2523
  51. Hinshaw, S.M. , and Harrison, S.C. (2019). The structure of the Ctf19c/CCAN from budding yeast. eLife 8. · DOI
  52. 10.1083/jcb.201403081 · DOI
  53. 10.1083/jcb.145.1.15 · DOI
  54. 1991, In vivo analysis of the Saccharomyces cerevisiae centromere CDEIII sequence: requirements for mitotic chromosome segregation, Molecular and cellular biology, 11, 5212
  55. 10.1038/ncb1414 · DOI
  56. 10.1128/MCB.19.9.6130 · DOI
  57. 10.1042/BCJ20210708 · DOI
  58. 10.1083/jcb.201412028 · DOI
  59. 1986, DNA bending at adenine, thymine tracts. Nature, 320, 501
  60. 10.1073/pnas.1118898109 · DOI
  61. Lang, J. , Barber, A. , and Biggins, S. (2018). An assay for de novo kinetochore assembly reveals a key role for the CENP-T pathway in budding yeast. eLife 7. · DOI
  62. 10.15252/embj.201798134 · DOI
  63. 10.1016/0092-8674(91)90501-O · DOI
  64. 2019, Structure of the Centromere Binding Factor 3 Complex from Kluyveromyces lactis, Journal of molecular biology, 431, 4444, 10.1016/j.jmb.2019.08.003 · DOI
  65. 10.1073/pnas.94.4.1183 · DOI
  66. 10.1093/bioinformatics/btt473 · DOI · Paper page
  67. 10.1093/nar/21.17.4133 · DOI
  68. 1986, Single base-pair mutations in centromere element III cause aberrant chromosome segregation in Saccharomyces cerevisiae, Molecular and cellular biology, 6, 530
  69. 1990, CPF1, a yeast protein which functions in centromeres and promoters, The EMBO journal, 9, 4017, 10.1002/j.1460-2075.1990.tb07623.x · DOI
  70. 10.1091/mbc.6.7.793 · DOI
  71. 10.1016/S0092-8674(00)81602-5 · DOI
  72. 10.1016/j.str.2019.12.002 · DOI
  73. 10.1007/BF00355368 · DOI
  74. Musacchio, A. , and Desai, A. (2017). A Molecular View of Kinetochore Assembly and Function. Biology 6. · DOI
  75. 2003, X-ray structures of Myc-Max and Mad-Max recognizing DNA, Molecular bases of regulation by proto-oncogenic transcription factors. Cell, 112, 193
  76. Navarro, A.P. , and Cheeseman, I.M. (2021). Kinetochore assembly throughout the cell cycle. Semin Cell Dev Biol. · DOI
  77. 10.1128/MCB.7.12.4522 · DOI
  78. 1991, In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1, Molecular and cellular biology, 11, 3545
  79. 10.1016/j.cell.2011.11.061 · DOI
  80. 10.1101/gad.13.9.1140 · DOI
  81. 1985, Role of conserved sequence elements in yeast centromere DNA, The EMBO journal, 4, 1867, 10.1002/j.1460-2075.1985.tb03862.x · DOI
  82. Pentakota, S. , Zhou, K. , Smith, C. , Maffini, S. , Petrovic, A. , Morgan, G.P. , Weir, J.R. , Vetter, I.R. , Musacchio, A. , and Luger, K. (2017). Decoding the centromeric nucleosome through CENP-N. eLife 6. · DOI
  83. 10.1128/MCB.05599-11 · DOI
  84. 2022, Structure of the human inner kinetochore CCAN complex and its significance for human centromere organization, Molecular cell, 82, 2113, 10.1016/j.molcel.2022.04.027 · DOI
  85. 10.1016/j.jsb.2015.08.008 · DOI
  86. 10.1073/pnas.1120968109 · DOI
  87. 10.1038/ncb2493 · DOI
  88. 10.1074/jbc.M110.183640 · DOI
  89. 10.1073/pnas.89.19.8908 · DOI
  90. 2022, Kinetochore Architecture Employs Diverse Linker Strategies Across Evolution, Front Cell Dev Biol, 10, 862637, 10.3389/fcell.2022.862637 · DOI
  91. 10.1101/gad.9.5.573 · DOI
  92. 2022, Structural insights into human CCAN complex assembled onto DNA, Cell Discov, 8, 90, 10.1038/s41421-022-00439-6 · DOI
  93. 10.1038/cr.2018.13 · DOI
  94. tunyasuvunakool, K. , Adler, J. , Wu, Z. , Green, T. , Zielinski, M. , Zidek, A. , Bridgland, A. , Cowie, A. , Meyer, C. , Laydon, A. , et al. (2021). Highly accurate protein structure prediction for the human proteome. Nature. · DOI · Paper page
  95. Walstein, K. , Petrovic, A. , Pan, D. , Hagemeier, B. , Vogt, D. , Vetter, I.R. , and Musacchio, A. (2021). Assembly principles and stoichiometry of a complete human kinetochore module. Sci Adv 7. · DOI
  96. 10.1093/bioinformatics/btp033 · DOI
  97. 10.1083/jcb.200305100 · DOI
  98. 10.1093/emboj/20.18.5207 · DOI
  99. 1996, The chromatin of the Saccharomyces cerevisiae centromere shows cell-type specific changes, Chromosoma, 104, 489
  100. 10.1083/jcb.129.6.1601 · DOI
  101. 10.7554/eLife.02203 · DOI
  102. 10.1101/gad.304782.117 · DOI
  103. 10.1038/s41586-019-1609-1 · DOI
  104. 2018, Architecture of the CBF3-centromere complex of the budding yeast kinetochore, Nature structural & molecular biology, 25, 1103, 10.1038/s41594-018-0154-1 · DOI
  105. 2022, Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome, Science, 376, 844, 10.1126/science.abn3810 · DOI · Paper page
  106. 2018, Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10, Cell reports, 24, 744, 10.1016/j.celrep.2018.06.068 · DOI
  107. 2020, Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex, Nucleic acids research, 48, 11172, 10.1093/nar/gkaa772 · DOI
  108. 10.1016/j.ymeth.2015.10.003 · DOI

Metadata

Authors
Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S. H., Schwab, J., Scheres, S. H. W., Yatskevich, S., & Barford, D.
Affiliations
MRC Laboratory of Molecular Biology (GB)
Corresponding author
Barford, David
ORCID
Venue
Science Advances
Publisher
openRxiv
Published
2022-12-12
Volume
9
Issue
30
Pages
eadg7480-eadg7480
ISSN
2375-2548 (ISSN-L)
DOI
10.1101/2022.12.12.520091
PMC
PMC10381965
OpenAlex
W4385334888
Cited by
58
References
1
Citations by year
2026: 16 · 2025: 26 · 2024: 11 · 2023: 5
FWCI
8.39
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Science Advances (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Wellcome Trust
  • Diamond Light Source (BI31336)
  • Alan Turing Institute (EP/W006022/1)
  • UK Research and Innovation (MC_UP_1201/6, EP/W006022/1)
  • Cancer Research UK (24307, C576/A14109, 14109)
  • Medical Research Council (MC_UP_1201/6)
  • Engineering and Physical Sciences Research Council (EP/W006022/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
inner kinetochore, Saccharomyces cerevisiae, CBF1, CBF3, KMN network, kinetochore assembly, chromosome segregation
MeSH terms
Centromere Protein A, Centromere, Chromosomal Proteins, Non-Histone, DNA, Saccharomycetales, Nuclear Proteins, Saccharomyces cerevisiae, Kinetochores, Cryoelectron Microscopy, Protein Subunits, Saccharomyces cerevisiae Proteins, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review