---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20935'
abstract:
- lang: eng
  text: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice
    to investigate the structures of biomolecules in their native context. However,
    challenges remain for the efficient production and sharing of large-scale cryo-ET
    datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB)
    milling with recent advances in cryo-ET acquisition and processing to generate
    a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii,
    which we provide as a community resource to drive method development and inspire
    biological discovery. To assay data quality, we performed subtomogram averaging
    of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200
    kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem
    II, and mitochondrial ATP synthase. The majority of these density maps reached
    sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset
    as well as the promise of modern cryo-ET workflows and open data sharing to empower
    visual proteomics.
acknowledgement: Calculations were performed at the Max Planck Institute of Biochemistry
  and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF)
  in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing
  center at the University of Basel, Switzerland; and at Thermo Fisher Scientific,
  in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific.
  All lamella preparations and tilt-series collections used in this work were conducted
  at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios
  microscopes. This work was also supported by the ERC consolidator grant “cryOcean”
  (fulfilled by the Swiss State Secretariat for Education, Research and Innovation,
  M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E.
  and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T.,
  an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim
  Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ron
  full_name: Kelley, Ron
  last_name: Kelley
- first_name: Sagar
  full_name: Khavnekar, Sagar
  last_name: Khavnekar
- first_name: Ricardo D.
  full_name: Righetto, Ricardo D.
  last_name: Righetto
- first_name: Jessica
  full_name: Heebner, Jessica
  last_name: Heebner
- first_name: Martin
  full_name: Obr, Martin
  id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
  last_name: Obr
  orcid: 0000-0003-1756-6564
- first_name: Xianjun
  full_name: Zhang, Xianjun
  last_name: Zhang
- first_name: Saikat
  full_name: Chakraborty, Saikat
  last_name: Chakraborty
- first_name: Grigory
  full_name: Tagiltsev, Grigory
  last_name: Tagiltsev
- first_name: Alicia
  full_name: Michael, Alicia
  id: 6437c950-2a03-11ee-914d-d6476dd7b75c
  last_name: Michael
  orcid: 0000-0002-6080-839X
- first_name: Sofie
  full_name: Van Dorst, Sofie
  last_name: Van Dorst
- first_name: Florent
  full_name: Waltz, Florent
  last_name: Waltz
- first_name: Caitlyn L.
  full_name: Mccafferty, Caitlyn L.
  last_name: Mccafferty
- first_name: Lorenz
  full_name: Lamm, Lorenz
  last_name: Lamm
- first_name: Simon
  full_name: Zufferey, Simon
  last_name: Zufferey
- first_name: Philippe
  full_name: Van Der Stappen, Philippe
  last_name: Van Der Stappen
- first_name: Hugo
  full_name: Van Den Hoek, Hugo
  last_name: Van Den Hoek
- first_name: Wojciech
  full_name: Wietrzynski, Wojciech
  last_name: Wietrzynski
- first_name: Pavol
  full_name: Harar, Pavol
  id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
  last_name: Harar
  orcid: 0000-0001-5206-1794
- first_name: William
  full_name: Wan, William
  last_name: Wan
- first_name: John A.G.
  full_name: Briggs, John A.G.
  last_name: Briggs
- first_name: Jürgen M.
  full_name: Plitzko, Jürgen M.
  last_name: Plitzko
- first_name: Benjamin D.
  full_name: Engel, Benjamin D.
  last_name: Engel
- first_name: Abhay
  full_name: Kotecha, Abhay
  last_name: Kotecha
citation:
  ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics
    with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular
    Cell</i>. doi:<a href="https://doi.org/10.1016/j.molcel.2025.11.029">10.1016/j.molcel.2025.11.029</a>
  apa: Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X.,
    … Kotecha, A. (n.d.). Toward community-driven visual proteomics with large-scale
    cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.molcel.2025.11.029">https://doi.org/10.1016/j.molcel.2025.11.029</a>
  chicago: Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin
    Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual
    Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.”
    <i>Molecular Cell</i>. Elsevier, n.d. <a href="https://doi.org/10.1016/j.molcel.2025.11.029">https://doi.org/10.1016/j.molcel.2025.11.029</a>.
  ieee: R. Kelley <i>et al.</i>, “Toward community-driven visual proteomics with large-scale
    cryo-electron tomography of Chlamydomonas reinhardtii,” <i>Molecular Cell</i>.
    Elsevier.
  ista: Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty
    S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey
    S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG,
    Plitzko JM, Engel BD, Kotecha A. Toward community-driven visual proteomics with
    large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.
  mla: Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale
    Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>,
    Elsevier, doi:<a href="https://doi.org/10.1016/j.molcel.2025.11.029">10.1016/j.molcel.2025.11.029</a>.
  short: R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S.
    Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty,
    L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P.
    Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular
    Cell (n.d.).
date_created: 2026-01-04T23:01:36Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-01-05T08:32:47Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.11.029
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.molcel.2025.11.029
month: '12'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
  eissn:
  - 1097-4164
  issn:
  - 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward community-driven visual proteomics with large-scale cryo-electron tomography
  of Chlamydomonas reinhardtii
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
_id: '18072'
abstract:
- lang: eng
  text: The individualization of chromosomes during early mitosis and their clustering
    upon exit from cell division are two key transitions that ensure efficient segregation
    of eukaryotic chromosomes. Both processes are regulated by the surfactant-like
    protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown.
    Here, we report that Ki-67 radically switches from a chromosome repellent to a
    chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation
    during mitotic exit and the simultaneous exposure of a conserved basic patch induce
    the RNA-dependent formation of a liquid-like condensed phase on the chromosome
    surface. Experiments and coarse-grained simulations support a model in which the
    coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA,
    promotes clustering of chromosomes. Our study reveals how the switch of Ki-67
    from a surfactant to a liquid-like condensed phase can generate mechanical forces
    during genome segregation that are required for re-establishing nuclear-cytoplasmic
    compartmentalization after mitosis.
acknowledgement: We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced
  Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail
  for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs.
  This work was supported by the German Research Foundation (DFG project number 402723784)
  and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received
  PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported
  by the European Research Council (ERC) under the European Union’s Horizon 2020 research
  and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship
  from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie
  Actions, COFUND grant agreement 664726).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Alberto
  full_name: Hernandez-Armendariz, Alberto
  last_name: Hernandez-Armendariz
- first_name: Valerio
  full_name: Sorichetti, Valerio
  id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
  last_name: Sorichetti
  orcid: 0000-0002-9645-6576
- first_name: Yuki
  full_name: Hayashi, Yuki
  last_name: Hayashi
- first_name: Zuzana
  full_name: Koskova, Zuzana
  last_name: Koskova
- first_name: Andreas
  full_name: Brunner, Andreas
  last_name: Brunner
- first_name: Jan
  full_name: Ellenberg, Jan
  last_name: Ellenberg
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
- first_name: Sara
  full_name: Cuylen-Haering, Sara
  last_name: Cuylen-Haering
citation:
  ama: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat
    mediates chromosome clustering during mitotic exit. <i>Molecular Cell</i>. 2024;84(17):P3254-3270.E9.
    doi:<a href="https://doi.org/10.1016/j.molcel.2024.07.022">10.1016/j.molcel.2024.07.022</a>
  apa: Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner,
    A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome
    clustering during mitotic exit. <i>Molecular Cell</i>. Cell Press. <a href="https://doi.org/10.1016/j.molcel.2024.07.022">https://doi.org/10.1016/j.molcel.2024.07.022</a>
  chicago: Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana
    Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering.
    “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” <i>Molecular
    Cell</i>. Cell Press, 2024. <a href="https://doi.org/10.1016/j.molcel.2024.07.022">https://doi.org/10.1016/j.molcel.2024.07.022</a>.
  ieee: A. Hernandez-Armendariz <i>et al.</i>, “A liquid-like coat mediates chromosome
    clustering during mitotic exit,” <i>Molecular Cell</i>, vol. 84, no. 17. Cell
    Press, p. P3254–3270.E9, 2024.
  ista: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg
    J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering
    during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9.
  mla: Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome
    Clustering during Mitotic Exit.” <i>Molecular Cell</i>, vol. 84, no. 17, Cell
    Press, 2024, p. P3254–3270.E9, doi:<a href="https://doi.org/10.1016/j.molcel.2024.07.022">10.1016/j.molcel.2024.07.022</a>.
  short: A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner,
    J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9.
date_created: 2024-09-15T22:01:41Z
date_published: 2024-09-05T00:00:00Z
date_updated: 2025-09-08T09:23:02Z
day: '05'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.molcel.2024.07.022
ec_funded: 1
external_id:
  isi:
  - '001309051100001'
  pmid:
  - '39153474'
file:
- access_level: open_access
  checksum: 3f360e0287b8ec79fb2b8b02b5070360
  content_type: application/pdf
  creator: dernst
  date_created: 2024-09-16T07:38:38Z
  date_updated: 2024-09-16T07:38:38Z
  file_id: '18075'
  file_name: 2024_MolecularCell_HernandezArmendariz.pdf
  file_size: 11654644
  relation: main_file
  success: 1
file_date_updated: 2024-09-16T07:38:38Z
has_accepted_license: '1'
intvolume: '        84'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: P3254-3270.E9
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
  call_identifier: H2020
  grant_number: '802960'
  name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Molecular Cell
publication_identifier:
  eissn:
  - 1097-4164
  issn:
  - 1097-2765
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: A liquid-like coat mediates chromosome clustering during mitotic exit
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 84
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9526'
abstract:
- lang: eng
  text: DNA methylation and histone H1 mediate transcriptional silencing of genes
    and transposable elements, but how they interact is unclear. In plants and animals
    with mosaic genomic methylation, functionally mysterious methylation is also common
    within constitutively active housekeeping genes. Here, we show that H1 is enriched
    in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment
    is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally
    alters nucleosome organization, and activates H1-bound genes, but only weakly
    de-represses transposable elements. However, H1 loss strongly activates transposable
    elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation
    of genes also activates antisense transcription, which is modestly enhanced by
    H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain
    transcriptional homeostasis by silencing transposable elements and aberrant intragenic
    transcripts. Such functionality plausibly explains why DNA methylation, a well-known
    mutagen, has been maintained within coding sequences of crucial plant and animal
    genes.
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
  full_name: Choi, Jaemyung
  last_name: Choi
- first_name: David B.
  full_name: Lyons, David B.
  last_name: Lyons
- first_name: M. Yvonne
  full_name: Kim, M. Yvonne
  last_name: Kim
- first_name: Jonathan D.
  full_name: Moore, Jonathan D.
  last_name: Moore
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone
    H1 jointly repress transposable elements and aberrant intragenic transcripts.
    <i>Molecular Cell</i>. 2020;77(2):310-323.e7. doi:<a href="https://doi.org/10.1016/j.molcel.2019.10.011">10.1016/j.molcel.2019.10.011</a>
  apa: Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., &#38; Zilberman, D. (2020).
    DNA methylation and histone H1 jointly repress transposable elements and aberrant
    intragenic transcripts. <i>Molecular Cell</i>. Elsevier. <a href="https://doi.org/10.1016/j.molcel.2019.10.011">https://doi.org/10.1016/j.molcel.2019.10.011</a>
  chicago: Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel
    Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements
    and Aberrant Intragenic Transcripts.” <i>Molecular Cell</i>. Elsevier, 2020. <a
    href="https://doi.org/10.1016/j.molcel.2019.10.011">https://doi.org/10.1016/j.molcel.2019.10.011</a>.
  ieee: J. Choi, D. B. Lyons, M. Y. Kim, J. D. Moore, and D. Zilberman, “DNA methylation
    and histone H1 jointly repress transposable elements and aberrant intragenic transcripts,”
    <i>Molecular Cell</i>, vol. 77, no. 2. Elsevier, p. 310–323.e7, 2020.
  ista: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA methylation and
    histone H1 jointly repress transposable elements and aberrant intragenic transcripts.
    Molecular Cell. 77(2), 310–323.e7.
  mla: Choi, Jaemyung, et al. “DNA Methylation and Histone H1 Jointly Repress Transposable
    Elements and Aberrant Intragenic Transcripts.” <i>Molecular Cell</i>, vol. 77,
    no. 2, Elsevier, 2020, p. 310–323.e7, doi:<a href="https://doi.org/10.1016/j.molcel.2019.10.011">10.1016/j.molcel.2019.10.011</a>.
  short: J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77
    (2020) 310–323.e7.
date_created: 2021-06-08T06:37:09Z
date_published: 2020-01-16T00:00:00Z
date_updated: 2024-10-16T12:14:37Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.molcel.2019.10.011
extern: '1'
external_id:
  pmid:
  - '31732458'
intvolume: '        77'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.molcel.2019.10.011
month: '01'
oa: 1
oa_version: Published Version
page: 310-323.e7
pmid: 1
publication: Molecular Cell
publication_identifier:
  eissn:
  - 1097-4164
  issn:
  - 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation and histone H1 jointly repress transposable elements and aberrant
  intragenic transcripts
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 77
year: '2020'
...