[{"publication_status":"inpress","language":[{"iso":"eng"}],"department":[{"_id":"AlMi"}],"date_created":"2026-01-04T23:01:36Z","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","author":[{"last_name":"Kelley","full_name":"Kelley, Ron","first_name":"Ron"},{"first_name":"Sagar","full_name":"Khavnekar, Sagar","last_name":"Khavnekar"},{"first_name":"Ricardo D.","full_name":"Righetto, Ricardo D.","last_name":"Righetto"},{"last_name":"Heebner","full_name":"Heebner, Jessica","first_name":"Jessica"},{"first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Xianjun","last_name":"Zhang","full_name":"Zhang, Xianjun"},{"full_name":"Chakraborty, Saikat","last_name":"Chakraborty","first_name":"Saikat"},{"first_name":"Grigory","full_name":"Tagiltsev, Grigory","last_name":"Tagiltsev"},{"orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","full_name":"Michael, Alicia","last_name":"Michael"},{"first_name":"Sofie","full_name":"Van Dorst, Sofie","last_name":"Van Dorst"},{"first_name":"Florent","last_name":"Waltz","full_name":"Waltz, Florent"},{"full_name":"Mccafferty, Caitlyn L.","last_name":"Mccafferty","first_name":"Caitlyn L."},{"full_name":"Lamm, Lorenz","last_name":"Lamm","first_name":"Lorenz"},{"first_name":"Simon","last_name":"Zufferey","full_name":"Zufferey, Simon"},{"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","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","last_name":"Harar","full_name":"Harar, Pavol","orcid":"0000-0001-5206-1794"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"first_name":"John A.G.","last_name":"Briggs","full_name":"Briggs, John A.G."},{"first_name":"Jürgen M.","full_name":"Plitzko, Jürgen M.","last_name":"Plitzko"},{"full_name":"Engel, Benjamin D.","last_name":"Engel","first_name":"Benjamin D."},{"first_name":"Abhay","last_name":"Kotecha","full_name":"Kotecha, Abhay"}],"publication":"Molecular Cell","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"oa":1,"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.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2025.11.029"}],"ddc":["570"],"doi":"10.1016/j.molcel.2025.11.029","OA_place":"publisher","article_type":"original","OA_type":"hybrid","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","month":"12","_id":"20935","citation":{"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.","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>.","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>","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>","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.","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.).","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>."},"PlanS_conform":"1","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","year":"2025","date_updated":"2026-01-05T08:32:47Z","date_published":"2025-12-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","publisher":"Elsevier","day":"19","type":"journal_article"},{"year":"2024","oa_version":"Published Version","date_updated":"2025-09-08T09:23:02Z","date_published":"2024-09-05T00:00:00Z","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"has_accepted_license":"1","page":"P3254-3270.E9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","publisher":"Cell Press","type":"journal_article","day":"05","issue":"17","ddc":["570"],"doi":"10.1016/j.molcel.2024.07.022","article_type":"original","title":"A liquid-like coat mediates chromosome clustering during mitotic exit","month":"09","_id":"18072","citation":{"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.","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.","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>","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>","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.","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>."},"article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"intvolume":"        84","isi":1,"file_date_updated":"2024-09-16T07:38:38Z","scopus_import":"1","publication":"Molecular Cell","author":[{"last_name":"Hernandez-Armendariz","full_name":"Hernandez-Armendariz, Alberto","first_name":"Alberto"},{"orcid":"0000-0002-9645-6576","last_name":"Sorichetti","full_name":"Sorichetti, Valerio","first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"first_name":"Yuki","last_name":"Hayashi","full_name":"Hayashi, Yuki"},{"last_name":"Koskova","full_name":"Koskova, Zuzana","first_name":"Zuzana"},{"first_name":"Andreas","full_name":"Brunner, Andreas","last_name":"Brunner"},{"first_name":"Jan","last_name":"Ellenberg","full_name":"Ellenberg, Jan"},{"last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"last_name":"Cuylen-Haering","full_name":"Cuylen-Haering, Sara","first_name":"Sara"}],"publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"oa":1,"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).","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":11654644,"creator":"dernst","file_name":"2024_MolecularCell_HernandezArmendariz.pdf","file_id":"18075","date_created":"2024-09-16T07:38:38Z","date_updated":"2024-09-16T07:38:38Z","checksum":"3f360e0287b8ec79fb2b8b02b5070360","content_type":"application/pdf"}],"pmid":1,"publication_status":"published","language":[{"iso":"eng"}],"external_id":{"pmid":["39153474"],"isi":["001309051100001"]},"department":[{"_id":"AnSa"}],"date_created":"2024-09-15T22:01:41Z","quality_controlled":"1","volume":84,"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."}]},{"publication":"Molecular Cell","author":[{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"last_name":"Lyons","full_name":"Lyons, David B.","first_name":"David B."},{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Jonathan D.","full_name":"Moore, Jonathan D.","last_name":"Moore"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"scopus_import":"1","intvolume":"        77","pmid":1,"oa":1,"publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2019.10.011","open_access":"1"}],"publication_status":"published","date_created":"2021-06-08T06:37:09Z","external_id":{"pmid":["31732458"]},"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"volume":77,"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"date_published":"2020-01-16T00:00:00Z","date_updated":"2024-10-16T12:14:37Z","year":"2020","oa_version":"Published Version","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","page":"310-323.e7","extern":"1","status":"public","issue":"2","type":"journal_article","publisher":"Elsevier","day":"16","article_type":"original","OA_type":"hybrid","OA_place":"publisher","doi":"10.1016/j.molcel.2019.10.011","_id":"9526","month":"01","title":"DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts","article_processing_charge":"No","citation":{"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>","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>","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.","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>.","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.","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."}}]