[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2026.01.021","pmid":1,"OA_type":"hybrid","month":"02","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2026-02-19T00:00:00Z","status":"public","ddc":["570"],"abstract":[{"text":"Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes.","lang":"eng"}],"publication_status":"published","file":[{"date_updated":"2026-03-30T12:04:38Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2026-03-30T12:04:38Z","file_id":"21510","checksum":"e16a7315b64a706184b177ea1621523c","success":1,"file_size":9786677,"file_name":"2026_MolecularCell_Weiss.pdf"}],"day":"19","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2026-03-30T12:09:08Z","issue":"4","department":[{"_id":"AlMi"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2026-03-30T11:58:48Z","acknowledgement":"We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada, D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance for critical discussions; and members of the Thomä lab for helpful feedback. Support for this work was provided to N.H.T. by the European Research Council under the European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852, and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS, no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden (25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported by an EMBO fellowship (ALTF 549-2021).","publication_identifier":{"issn":["1097-2765"]},"volume":86,"external_id":{"pmid":["41679301"]},"title":"The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2","article_type":"original","publication":"Molecular Cell","year":"2026","OA_place":"publisher","page":"625-639.e8","type":"journal_article","intvolume":"        86","publisher":"Elsevier","PlanS_conform":"1","_id":"21509","file_date_updated":"2026-03-30T12:04:38Z","author":[{"last_name":"Weiss","first_name":"Joscha","full_name":"Weiss, Joscha"},{"first_name":"Luca","last_name":"Vecchia","full_name":"Vecchia, Luca"},{"full_name":"Domjan, David","last_name":"Domjan","first_name":"David"},{"full_name":"Cavadini, Simone","first_name":"Simone","last_name":"Cavadini"},{"last_name":"Sabantsev","first_name":"Anton","full_name":"Sabantsev, Anton"},{"full_name":"Kempf, Georg","last_name":"Kempf","first_name":"Georg"},{"last_name":"Pathare","first_name":"Ganesh R.","full_name":"Pathare, Ganesh R."},{"first_name":"Klaus","last_name":"Brackmann","full_name":"Brackmann, Klaus"},{"orcid":"0000-0002-6080-839X","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","full_name":"Michael, Alicia"},{"full_name":"Kater, Lukas","first_name":"Lukas","last_name":"Kater"},{"first_name":"Eric","last_name":"Hietter-Pfeiffer","full_name":"Hietter-Pfeiffer, Eric"},{"last_name":"Haddawi","first_name":"Mina","full_name":"Haddawi, Mina"},{"full_name":"Kuber, Urja P.","last_name":"Kuber","first_name":"Urja P."},{"first_name":"Sandra","last_name":"Mühlhäusser","full_name":"Mühlhäusser, Sandra"},{"first_name":"Ralph S.","last_name":"Grand","full_name":"Grand, Ralph S."},{"full_name":"Stadler, Michael B.","first_name":"Michael B.","last_name":"Stadler"},{"full_name":"Deindl, Sebastian","last_name":"Deindl","first_name":"Sebastian"},{"full_name":"Thomä, Nicolas H.","first_name":"Nicolas H.","last_name":"Thomä"}],"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"ieee":"J. Weiss <i>et al.</i>, “The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2,” <i>Molecular Cell</i>, vol. 86, no. 4. Elsevier, p. 625–639.e8, 2026.","ista":"Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 86(4), 625–639.e8.","mla":"Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>, vol. 86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>.","ama":"Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. 2026;86(4):625-639.e8. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>","apa":"Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G., … Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>","short":"J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R. Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi, U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular Cell 86 (2026) 625–639.e8.","chicago":"Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev, Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>."}},{"_id":"20374","file_date_updated":"2025-09-24T07:54:03Z","author":[{"first_name":"Deyasini","last_name":"Chakraborty","full_name":"Chakraborty, Deyasini"},{"last_name":"Sandate","first_name":"Colby R.","full_name":"Sandate, Colby R."},{"last_name":"Isbel","first_name":"Luke","full_name":"Isbel, Luke"},{"first_name":"Georg","last_name":"Kempf","full_name":"Kempf, Georg"},{"first_name":"Joscha","last_name":"Weiss","full_name":"Weiss, Joscha"},{"full_name":"Cavadini, Simone","first_name":"Simone","last_name":"Cavadini"},{"last_name":"Kater","first_name":"Lukas","full_name":"Kater, Lukas"},{"full_name":"Seebacher, Jan","first_name":"Jan","last_name":"Seebacher"},{"full_name":"Kozicka, Zuzanna","first_name":"Zuzanna","last_name":"Kozicka"},{"first_name":"Lisa","last_name":"Stoos","full_name":"Stoos, Lisa"},{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"first_name":"Dirk","last_name":"Schübeler","full_name":"Schübeler, Dirk"},{"full_name":"Michael, Alicia","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","orcid":"0000-0002-6080-839X","first_name":"Alicia"},{"last_name":"Thomä","first_name":"Nicolas H.","full_name":"Thomä, Nicolas H."}],"citation":{"mla":"Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.” <i>Molecular Cell</i>, vol. 85, no. 15, Elsevier, 2025, p. 2919–2936.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">10.1016/j.molcel.2025.06.027</a>.","ista":"Chakraborty D, Sandate CR, Isbel L, Kempf G, Weiss J, Cavadini S, Kater L, Seebacher J, Kozicka Z, Stoos L, Grand RS, Schübeler D, Michael AK, Thomä NH. 2025. Nucleosomes specify co-factor access to p53. Molecular Cell. 85(15), 2919–2936.e12.","ieee":"D. Chakraborty <i>et al.</i>, “Nucleosomes specify co-factor access to p53,” <i>Molecular Cell</i>, vol. 85, no. 15. Elsevier, p. 2919–2936.e12, 2025.","ama":"Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access to p53. <i>Molecular Cell</i>. 2025;85(15):2919-2936.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">10.1016/j.molcel.2025.06.027</a>","short":"D. Chakraborty, C.R. Sandate, L. Isbel, G. Kempf, J. Weiss, S. Cavadini, L. Kater, J. Seebacher, Z. Kozicka, L. Stoos, R.S. Grand, D. Schübeler, A.K. Michael, N.H. Thomä, Molecular Cell 85 (2025) 2919–2936.e12.","apa":"Chakraborty, D., Sandate, C. R., Isbel, L., Kempf, G., Weiss, J., Cavadini, S., … Thomä, N. H. (2025). Nucleosomes specify co-factor access to p53. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">https://doi.org/10.1016/j.molcel.2025.06.027</a>","chicago":"Chakraborty, Deyasini, Colby R. Sandate, Luke Isbel, Georg Kempf, Joscha Weiss, Simone Cavadini, Lukas Kater, et al. “Nucleosomes Specify Co-Factor Access to P53.” <i>Molecular Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.molcel.2025.06.027\">https://doi.org/10.1016/j.molcel.2025.06.027</a>."},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","type":"journal_article","publisher":"Elsevier","PlanS_conform":"1","intvolume":"        85","publication":"Molecular Cell","year":"2025","volume":85,"title":"Nucleosomes specify co-factor access to p53","article_type":"original","page":"2919-2936.e12","OA_place":"publisher","department":[{"_id":"AlMi"}],"publication_identifier":{"issn":["1097-2765"]},"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We thank M. Schütz for laboratory management, organization, and assistance with manuscript editing. We are grateful to all Thomä and Schübeler lab members. We thank Ulrich Hassiepen from Novartis for his support and insightful discussions on the kinetic analysis. This work was supported by funding from the European Research Council (ERC), under the European Union’s H2020 research program (NucEM, grant no. 884331); the Swiss National Science Foundation (SNF, grant no. 310030_301206 and 310030_214852); Krebsforschung (KFS, grant no. KFS-5933-08-2023); Novartis Research Foundation (to N.H.T.); the Novartis Freenovation (grant no. FN23-0000000514 to C.R.S.); the National Health and Medical Research Council CJ Martin Fellowship (APP1148380); the EU Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant (grant no. 748760); the South Australian immunoGENomics Cancer Institute grant funding from the Australian Government; and the Sylvia and Charles Viertel Charitable Foundation Senior Medical Research Fellowship (to L.I.).","date_created":"2025-09-23T08:56:13Z","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2025-09-24T08:21:55Z","issue":"15","file":[{"success":1,"file_name":"2025_MolecularCell_Chakraborty.pdf","file_size":41813494,"checksum":"e60390ca629b350af3221d4718ca6534","date_created":"2025-09-24T07:54:03Z","file_id":"20386","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-09-24T07:54:03Z"}],"day":"07","status":"public","date_published":"2025-08-07T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However, it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors. In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring inaccessible chromatin. We examined the interaction of chromatin-bound p53 with co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct motif locations on the nucleosome (super-helical location [SHL]−5.7 and SHL+5.9), the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered interaction domains of co-factors and TFs govern compatibility between co-factors, TFs, and chromatin."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2025.06.027","month":"08","OA_type":"hybrid","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"day":"19","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2026-01-05T08:32:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2025.11.029","OA_type":"hybrid","month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2025.11.029","open_access":"1"}],"date_published":"2025-12-19T00:00:00Z","status":"public","ddc":["570"],"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"}],"publication_status":"inpress","type":"journal_article","publisher":"Elsevier","PlanS_conform":"1","_id":"20935","author":[{"full_name":"Kelley, Ron","first_name":"Ron","last_name":"Kelley"},{"full_name":"Khavnekar, Sagar","first_name":"Sagar","last_name":"Khavnekar"},{"full_name":"Righetto, Ricardo D.","last_name":"Righetto","first_name":"Ricardo D."},{"full_name":"Heebner, Jessica","first_name":"Jessica","last_name":"Heebner"},{"full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"first_name":"Xianjun","last_name":"Zhang","full_name":"Zhang, Xianjun"},{"full_name":"Chakraborty, Saikat","last_name":"Chakraborty","first_name":"Saikat"},{"full_name":"Tagiltsev, Grigory","first_name":"Grigory","last_name":"Tagiltsev"},{"orcid":"0000-0002-6080-839X","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","full_name":"Michael, Alicia"},{"full_name":"Van Dorst, Sofie","first_name":"Sofie","last_name":"Van Dorst"},{"last_name":"Waltz","first_name":"Florent","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"},{"full_name":"Zufferey, Simon","last_name":"Zufferey","first_name":"Simon"},{"first_name":"Philippe","last_name":"Van Der Stappen","full_name":"Van Der Stappen, Philippe"},{"full_name":"Van Den Hoek, Hugo","first_name":"Hugo","last_name":"Van Den Hoek"},{"full_name":"Wietrzynski, Wojciech","first_name":"Wojciech","last_name":"Wietrzynski"},{"full_name":"Harar, Pavol","first_name":"Pavol","orcid":"0000-0001-5206-1794","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","last_name":"Harar"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"full_name":"Briggs, John A.G.","last_name":"Briggs","first_name":"John A.G."},{"full_name":"Plitzko, Jürgen M.","first_name":"Jürgen M.","last_name":"Plitzko"},{"last_name":"Engel","first_name":"Benjamin D.","full_name":"Engel, Benjamin D."},{"full_name":"Kotecha, Abhay","last_name":"Kotecha","first_name":"Abhay"}],"quality_controlled":"1","scopus_import":"1","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>","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.","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>.","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>.","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.).","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>"},"department":[{"_id":"AlMi"}],"article_processing_charge":"Yes (in subscription journal)","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.","date_created":"2026-01-04T23:01:36Z","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"article_type":"original","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","publication":"Molecular Cell","year":"2025","OA_place":"publisher"},{"day":"05","file":[{"date_updated":"2024-09-16T07:38:38Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2024-09-16T07:38:38Z","file_id":"18075","checksum":"3f360e0287b8ec79fb2b8b02b5070360","success":1,"file_name":"2024_MolecularCell_HernandezArmendariz.pdf","file_size":11654644}],"date_updated":"2025-09-08T09:23:02Z","oa_version":"Published Version","issue":"17","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"doi":"10.1016/j.molcel.2024.07.022","ddc":["570"],"publication_status":"published","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."}],"date_published":"2024-09-05T00:00:00Z","status":"public","intvolume":"        84","publisher":"Cell Press","isi":1,"type":"journal_article","scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","citation":{"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.","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>.","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>.","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.","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>"},"file_date_updated":"2024-09-16T07:38:38Z","_id":"18072","author":[{"full_name":"Hernandez-Armendariz, Alberto","last_name":"Hernandez-Armendariz","first_name":"Alberto"},{"orcid":"0000-0002-9645-6576","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti","first_name":"Valerio","full_name":"Sorichetti, Valerio"},{"first_name":"Yuki","last_name":"Hayashi","full_name":"Hayashi, Yuki"},{"last_name":"Koskova","first_name":"Zuzana","full_name":"Koskova, Zuzana"},{"first_name":"Andreas","last_name":"Brunner","full_name":"Brunner, Andreas"},{"last_name":"Ellenberg","first_name":"Jan","full_name":"Ellenberg, Jan"},{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"last_name":"Cuylen-Haering","first_name":"Sara","full_name":"Cuylen-Haering, Sara"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-09-15T22:01:41Z","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).","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"department":[{"_id":"AnSa"}],"page":"P3254-3270.E9","volume":84,"article_type":"original","external_id":{"pmid":["39153474"],"isi":["001309051100001"]},"title":"A liquid-like coat mediates chromosome clustering during mitotic exit","project":[{"grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"publication":"Molecular Cell","year":"2024"},{"publication":"Molecular Cell","year":"2024","volume":84,"article_type":"original","external_id":{"isi":["001395711300001"],"pmid":["39547223"]},"title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","page":"4740-4757.e12","OA_place":"publisher","department":[{"_id":"CaBe"}],"publication_identifier":{"issn":["1097-2765"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"article_processing_charge":"No","acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","date_created":"2024-11-15T12:12:54Z","file_date_updated":"2025-01-13T11:17:35Z","_id":"18553","author":[{"full_name":"Ramadhin, Anisha R.","first_name":"Anisha R.","last_name":"Ramadhin"},{"full_name":"Lee, Shun-Hsiao","last_name":"Lee","first_name":"Shun-Hsiao"},{"full_name":"Zhou, Di","last_name":"Zhou","first_name":"Di"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"last_name":"Gonzalo-Hansen","first_name":"Camila","full_name":"Gonzalo-Hansen, Camila"},{"full_name":"van Sluis, Marjolein","last_name":"van Sluis","first_name":"Marjolein"},{"full_name":"Blom, Cindy M.A.","first_name":"Cindy M.A.","last_name":"Blom"},{"last_name":"Janssens","first_name":"Roel C.","full_name":"Janssens, Roel C."},{"full_name":"Raams, Anja","last_name":"Raams","first_name":"Anja"},{"last_name":"Dekkers","first_name":"Dick","full_name":"Dekkers, Dick"},{"full_name":"Bezstarosti, Karel","first_name":"Karel","last_name":"Bezstarosti"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"},{"last_name":"Vermeulen","first_name":"Wim","full_name":"Vermeulen, Wim"},{"full_name":"Pines, Alex","first_name":"Alex","last_name":"Pines"},{"full_name":"Demmers, Jeroen A.A.","first_name":"Jeroen A.A.","last_name":"Demmers"},{"first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"},{"full_name":"Sixma, Titia K.","last_name":"Sixma","first_name":"Titia K."},{"full_name":"Marteijn, Jurgen A.","last_name":"Marteijn","first_name":"Jurgen A."}],"citation":{"ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>","ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12."},"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","isi":1,"type":"journal_article","publisher":"Elsevier","intvolume":"        84","status":"public","date_published":"2024-12-19T00:00:00Z","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.molcel.2024.10.030","pmid":1,"OA_type":"hybrid","month":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-09-08T14:42:50Z","oa_version":"Published Version","issue":"24","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-13T11:17:35Z","creator":"dernst","access_level":"open_access","success":1,"file_size":25071994,"file_name":"2024_MolecularCell_Ramadhin.pdf","date_created":"2025-01-13T11:17:35Z","file_id":"18844","checksum":"e051e2766b2d424983778f742cb7c5ed"}],"day":"19"},{"publisher":"Elsevier","intvolume":"        83","type":"journal_article","keyword":["Cell Biology","Molecular Biology"],"citation":{"ieee":"R. E. O’Brien, J. P. K. Bravo, D. Ramos, G. N. Hibshman, J. T. Wright, and D. W. Taylor, “Structural snapshots of R-loop formation by a type I-C CRISPR Cascade,” <i>Molecular Cell</i>, vol. 83, no. 5. Elsevier, p. 746–758.e5, 2023.","ista":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. 2023. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Molecular Cell. 83(5), 746–758.e5.","mla":"O’Brien, Roisin E., et al. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” <i>Molecular Cell</i>, vol. 83, no. 5, Elsevier, 2023, p. 746–758.e5, doi:<a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">10.1016/j.molcel.2023.01.024</a>.","ama":"O’Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. <i>Molecular Cell</i>. 2023;83(5):746-758.e5. doi:<a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">10.1016/j.molcel.2023.01.024</a>","short":"R.E. O’Brien, J.P.K. Bravo, D. Ramos, G.N. Hibshman, J.T. Wright, D.W. Taylor, Molecular Cell 83 (2023) 746–758.e5.","apa":"O’Brien, R. E., Bravo, J. P. K., Ramos, D., Hibshman, G. N., Wright, J. T., &#38; Taylor, D. W. (2023). Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">https://doi.org/10.1016/j.molcel.2023.01.024</a>","chicago":"O’Brien, Roisin E., Jack Peter Kelly Bravo, Delisa Ramos, Grace N. Hibshman, Jacquelyn T. Wright, and David W. Taylor. “Structural Snapshots of R-Loop Formation by a Type I-C CRISPR Cascade.” <i>Molecular Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.molcel.2023.01.024\">https://doi.org/10.1016/j.molcel.2023.01.024</a>."},"quality_controlled":"1","scopus_import":"1","_id":"15129","author":[{"last_name":"O’Brien","first_name":"Roisin E.","full_name":"O’Brien, Roisin E."},{"orcid":"0000-0003-0456-0753","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"last_name":"Ramos","first_name":"Delisa","full_name":"Ramos, Delisa"},{"last_name":"Hibshman","first_name":"Grace N.","full_name":"Hibshman, Grace N."},{"full_name":"Wright, Jacquelyn T.","last_name":"Wright","first_name":"Jacquelyn T."},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."}],"publication_identifier":{"issn":["1097-2765"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-03-20T10:40:56Z","page":"746-758.e5","publication":"Molecular Cell","year":"2023","volume":83,"title":"Structural snapshots of R-loop formation by a type I-C CRISPR Cascade","external_id":{"pmid":["36805026"]},"article_type":"original","day":"02","date_updated":"2024-06-04T06:33:54Z","oa_version":"Published Version","issue":"5","oa":1,"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2023.01.024"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1016/j.molcel.2023.01.024","extern":"1","publication_status":"published","abstract":[{"text":"Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the “belly” subunits, securing the NTS in place. This “molecular seatbelt” mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.","lang":"eng"}],"status":"public","date_published":"2023-03-02T00:00:00Z"},{"file":[{"date_updated":"2023-01-24T09:29:02Z","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"12354","date_created":"2023-01-24T09:29:02Z","checksum":"999e443b54e4fdaa2542ca5a97619731","file_size":7368534,"file_name":"2022_MolecularCell_Zapletal.pdf","success":1}],"day":"03","language":[{"iso":"eng"}],"oa":1,"issue":"21","date_updated":"2023-08-04T08:57:17Z","oa_version":"Published Version","doi":"10.1016/j.molcel.2022.10.010","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"11","date_published":"2022-11-03T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"ddc":["570"],"type":"journal_article","isi":1,"intvolume":"        82","publisher":"Elsevier","author":[{"full_name":"Zapletal, David","last_name":"Zapletal","first_name":"David"},{"last_name":"Taborska","first_name":"Eliska","full_name":"Taborska, Eliska"},{"first_name":"Josef","last_name":"Pasulka","full_name":"Pasulka, Josef"},{"first_name":"Radek","last_name":"Malik","full_name":"Malik, Radek"},{"first_name":"Karel","last_name":"Kubicek","full_name":"Kubicek, Karel"},{"full_name":"Zanova, Martina","first_name":"Martina","last_name":"Zanova"},{"full_name":"Much, Christian","first_name":"Christian","last_name":"Much"},{"last_name":"Sebesta","first_name":"Marek","full_name":"Sebesta, Marek"},{"full_name":"Buccheri, Valeria","first_name":"Valeria","last_name":"Buccheri"},{"first_name":"Filip","last_name":"Horvat","full_name":"Horvat, Filip"},{"last_name":"Jenickova","first_name":"Irena","full_name":"Jenickova, Irena"},{"last_name":"Prochazkova","first_name":"Michaela","full_name":"Prochazkova, Michaela"},{"full_name":"Prochazka, Jan","first_name":"Jan","last_name":"Prochazka"},{"full_name":"Pinkas, Matyas","first_name":"Matyas","last_name":"Pinkas"},{"full_name":"Novacek, Jiri","first_name":"Jiri","last_name":"Novacek"},{"last_name":"Joseph","first_name":"Diego F.","full_name":"Joseph, Diego F."},{"last_name":"Sedlacek","first_name":"Radislav","full_name":"Sedlacek, Radislav"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036","first_name":"Carrie A"},{"full_name":"O’Carroll, Dónal","last_name":"O’Carroll","first_name":"Dónal"},{"first_name":"Richard","last_name":"Stefl","full_name":"Stefl, Richard"},{"first_name":"Petr","last_name":"Svoboda","full_name":"Svoboda, Petr"}],"file_date_updated":"2023-01-24T09:29:02Z","_id":"12143","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>","chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>.","mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>.","ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","ieee":"D. Zapletal <i>et al.</i>, “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” <i>Molecular Cell</i>, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022.","ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. 2022;82(21):4064-4079.e13. doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>"},"keyword":["Cell Biology","Molecular Biology"],"department":[{"_id":"CaBe"}],"acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","date_created":"2023-01-12T12:05:36Z","article_processing_charge":"No","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1097-2765"]},"external_id":{"isi":["000898565300011"],"pmid":["36332606"]},"article_type":"original","title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","volume":82,"year":"2022","publication":"Molecular Cell","page":"4064-4079.e13"},{"intvolume":"        81","publisher":"Elsevier","type":"journal_article","quality_controlled":"1","scopus_import":"1","keyword":["Cell Biology","Molecular Biology"],"citation":{"ama":"Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. <i>Molecular Cell</i>. 2021;81(7):1548-1552.e4. doi:<a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">10.1016/j.molcel.2021.01.035</a>","mla":"Bravo, Jack Peter Kelly, et al. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” <i>Molecular Cell</i>, vol. 81, no. 7, Elsevier, 2021, p. 1548–1552.e4, doi:<a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">10.1016/j.molcel.2021.01.035</a>.","ieee":"J. P. K. Bravo, T. L. Dangerfield, D. W. Taylor, and K. A. Johnson, “Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication,” <i>Molecular Cell</i>, vol. 81, no. 7. Elsevier, p. 1548–1552.e4, 2021.","ista":"Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. 2021. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. 81(7), 1548–1552.e4.","chicago":"Bravo, Jack Peter Kelly, Tyler L. Dangerfield, David W. Taylor, and Kenneth A. Johnson. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” <i>Molecular Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">https://doi.org/10.1016/j.molcel.2021.01.035</a>.","short":"J.P.K. Bravo, T.L. Dangerfield, D.W. Taylor, K.A. Johnson, Molecular Cell 81 (2021) 1548–1552.e4.","apa":"Bravo, J. P. K., Dangerfield, T. L., Taylor, D. W., &#38; Johnson, K. A. (2021). Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">https://doi.org/10.1016/j.molcel.2021.01.035</a>"},"_id":"15140","author":[{"first_name":"Jack Peter Kelly","last_name":"Bravo","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly"},{"last_name":"Dangerfield","first_name":"Tyler L.","full_name":"Dangerfield, Tyler L."},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"full_name":"Johnson, Kenneth A.","last_name":"Johnson","first_name":"Kenneth A."}],"article_processing_charge":"No","date_created":"2024-03-20T10:42:53Z","publication_identifier":{"issn":["1097-2765"]},"page":"1548-1552.e4","volume":81,"external_id":{"pmid":["33631104"]},"article_type":"original","title":"Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication","publication":"Molecular Cell","year":"2021","day":"01","oa_version":"Preprint","date_updated":"2024-06-04T06:00:56Z","issue":"7","oa":1,"language":[{"iso":"eng"}],"month":"04","main_file_link":[{"url":"https://doi.org/10.1101/2020.12.14.422718 ","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2021.01.035","pmid":1,"extern":"1","abstract":[{"text":"Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.","lang":"eng"}],"publication_status":"published","date_published":"2021-04-01T00:00:00Z","status":"public"},{"department":[{"_id":"DaZi"}],"publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"article_processing_charge":"No","date_created":"2021-06-08T06:37:09Z","publication":"Molecular Cell","year":"2020","volume":77,"external_id":{"pmid":["31732458"]},"article_type":"original","title":"DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts","OA_place":"publisher","page":"310-323.e7","type":"journal_article","publisher":"Elsevier","intvolume":"        77","_id":"9526","author":[{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"last_name":"Lyons","first_name":"David B.","full_name":"Lyons, David B."},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Moore","first_name":"Jonathan D.","full_name":"Moore, Jonathan D."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"citation":{"short":"J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77 (2020) 310–323.e7.","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>.","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>.","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.","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>"},"quality_controlled":"1","scopus_import":"1","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","pmid":1,"doi":"10.1016/j.molcel.2019.10.011","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2019.10.011","open_access":"1"}],"month":"01","OA_type":"hybrid","status":"public","date_published":"2020-01-16T00:00:00Z","extern":"1","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."}],"publication_status":"published","day":"16","oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-10-16T12:14:37Z","oa_version":"Published Version","issue":"2"},{"publication_identifier":{"issn":["1097-2765"]},"article_processing_charge":"No","date_created":"2020-01-29T16:02:33Z","department":[{"_id":"LeSa"}],"page":"1131-1146.e6","project":[{"grant_number":"701309","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","name":"Atomic Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes"}],"publication":"Molecular Cell","year":"2019","volume":75,"title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","external_id":{"isi":["000486614200006"],"pmid":["31492636"]},"article_type":"original","publisher":"Cell Press","intvolume":"        75","isi":1,"type":"journal_article","citation":{"ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. <i>Molecular Cell</i>. 2019;75(6):1131-1146.e6. doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">10.1016/j.molcel.2019.07.022</a>","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” <i>Molecular Cell</i>, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019.","mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” <i>Molecular Cell</i>, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">10.1016/j.molcel.2019.07.022</a>.","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” <i>Molecular Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">https://doi.org/10.1016/j.molcel.2019.07.022</a>.","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., &#38; Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2019.07.022\">https://doi.org/10.1016/j.molcel.2019.07.022</a>","short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6."},"scopus_import":"1","quality_controlled":"1","has_accepted_license":"1","_id":"7395","file_date_updated":"2020-07-14T12:47:57Z","author":[{"full_name":"Letts, James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","last_name":"Letts","first_name":"James A"},{"first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol"},{"full_name":"Degliesposti, Gianluca","last_name":"Degliesposti","first_name":"Gianluca"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"month":"09","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1016/j.molcel.2019.07.022","pmid":1,"ddc":["570"],"publication_status":"published","abstract":[{"text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.","lang":"eng"}],"status":"public","date_published":"2019-09-19T00:00:00Z","day":"19","file":[{"file_size":9654895,"file_name":"2019_MolecularCell_Letts.pdf","file_id":"7447","date_created":"2020-02-04T10:37:28Z","checksum":"5202f53a237d6650ece038fbf13bdcea","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:57Z","access_level":"open_access","creator":"dernst"}],"corr_author":"1","date_updated":"2024-10-22T09:34:12Z","oa_version":"Published Version","issue":"6","ec_funded":1,"language":[{"iso":"eng"}],"oa":1},{"status":"public","date_published":"2017-05-18T00:00:00Z","extern":"1","abstract":[{"text":"The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2017.04.011","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2017.04.011","open_access":"1"}],"month":"05","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2024-03-25T12:19:20Z","issue":"4","day":"18","publication":"Molecular Cell","year":"2017","volume":66,"article_type":"original","title":"A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms","page":"447-457.e7","publication_identifier":{"issn":["1097-2765"]},"article_processing_charge":"No","date_created":"2024-03-21T07:56:01Z","_id":"15155","author":[{"last_name":"Gustafson","first_name":"Chelsea L.","full_name":"Gustafson, Chelsea L."},{"first_name":"Nicole C.","last_name":"Parsley","full_name":"Parsley, Nicole C."},{"first_name":"Hande","last_name":"Asimgil","full_name":"Asimgil, Hande"},{"first_name":"Hsiau-Wei","last_name":"Lee","full_name":"Lee, Hsiau-Wei"},{"last_name":"Ahlbach","first_name":"Christopher","full_name":"Ahlbach, Christopher"},{"first_name":"Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen"},{"full_name":"Xu, Haiyan","first_name":"Haiyan","last_name":"Xu"},{"first_name":"Owen L.","last_name":"Williams","full_name":"Williams, Owen L."},{"first_name":"Tara L.","last_name":"Davis","full_name":"Davis, Tara L."},{"full_name":"Liu, Andrew C.","first_name":"Andrew C.","last_name":"Liu"},{"first_name":"Carrie L.","last_name":"Partch","full_name":"Partch, Carrie L."}],"keyword":["Cell Biology","Molecular Biology"],"citation":{"ama":"Gustafson CL, Parsley NC, Asimgil H, et al. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. <i>Molecular Cell</i>. 2017;66(4):447-457.e7. doi:<a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">10.1016/j.molcel.2017.04.011</a>","ieee":"C. L. Gustafson <i>et al.</i>, “A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms,” <i>Molecular Cell</i>, vol. 66, no. 4. Elsevier, p. 447–457.e7, 2017.","mla":"Gustafson, Chelsea L., et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” <i>Molecular Cell</i>, vol. 66, no. 4, Elsevier, 2017, p. 447–457.e7, doi:<a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">10.1016/j.molcel.2017.04.011</a>.","ista":"Gustafson CL, Parsley NC, Asimgil H, Lee H-W, Ahlbach C, Michael AK, Xu H, Williams OL, Davis TL, Liu AC, Partch CL. 2017. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. 66(4), 447–457.e7.","chicago":"Gustafson, Chelsea L., Nicole C. Parsley, Hande Asimgil, Hsiau-Wei Lee, Christopher Ahlbach, Alicia K. Michael, Haiyan Xu, et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” <i>Molecular Cell</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">https://doi.org/10.1016/j.molcel.2017.04.011</a>.","short":"C.L. Gustafson, N.C. Parsley, H. Asimgil, H.-W. Lee, C. Ahlbach, A.K. Michael, H. Xu, O.L. Williams, T.L. Davis, A.C. Liu, C.L. Partch, Molecular Cell 66 (2017) 447–457.e7.","apa":"Gustafson, C. L., Parsley, N. C., Asimgil, H., Lee, H.-W., Ahlbach, C., Michael, A. K., … Partch, C. L. (2017). A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">https://doi.org/10.1016/j.molcel.2017.04.011</a>"},"scopus_import":"1","quality_controlled":"1","type":"journal_article","publisher":"Elsevier","intvolume":"        66"},{"type":"journal_article","intvolume":"        58","publisher":"Elsevier","_id":"15160","author":[{"full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"first_name":"Stacy L.","last_name":"Harvey","full_name":"Harvey, Stacy L."},{"full_name":"Sammons, Patrick J.","first_name":"Patrick J.","last_name":"Sammons"},{"full_name":"Anderson, Amanda P.","last_name":"Anderson","first_name":"Amanda P."},{"full_name":"Kopalle, Hema M.","first_name":"Hema M.","last_name":"Kopalle"},{"full_name":"Banham, Alison H.","first_name":"Alison H.","last_name":"Banham"},{"first_name":"Carrie L.","last_name":"Partch","full_name":"Partch, Carrie L."}],"quality_controlled":"1","scopus_import":"1","keyword":["Cell Biology","Molecular Biology"],"citation":{"chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” <i>Molecular Cell</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">https://doi.org/10.1016/j.molcel.2015.03.031</a>.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., &#38; Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">https://doi.org/10.1016/j.molcel.2015.03.031</a>","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. <i>Molecular Cell</i>. 2015;58(5):743-754. doi:<a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">10.1016/j.molcel.2015.03.031</a>","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754.","mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” <i>Molecular Cell</i>, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:<a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">10.1016/j.molcel.2015.03.031</a>.","ieee":"A. K. Michael <i>et al.</i>, “Cancer/Testis antigen PASD1 silences the circadian clock,” <i>Molecular Cell</i>, vol. 58, no. 5. Elsevier, pp. 743–754, 2015."},"article_processing_charge":"No","date_created":"2024-03-21T07:58:08Z","publication_identifier":{"issn":["1097-2765"]},"volume":58,"article_type":"original","title":"Cancer/Testis antigen PASD1 silences the circadian clock","publication":"Molecular Cell","year":"2015","page":"743-754","day":"04","oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-03-25T11:52:26Z","oa_version":"Published Version","issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2015.03.031","month":"06","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2015.03.031","open_access":"1"}],"date_published":"2015-06-04T00:00:00Z","status":"public","extern":"1","abstract":[{"text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.","lang":"eng"}],"publication_status":"published"},{"intvolume":"         5","publisher":"Elsevier","type":"journal_article","scopus_import":"1","quality_controlled":"1","citation":{"ama":"Hetzer M, Bilbao-Cortés D, Walther TC, Gruss OJ, Mattaj IW. GTP hydrolysis by Ran is required for nuclear envelope assembly. <i>Molecular Cell</i>. 2000;5(6):1013-1024. doi:<a href=\"https://doi.org/10.1016/s1097-2765(00)80266-x\">10.1016/s1097-2765(00)80266-x</a>","ieee":"M. Hetzer, D. Bilbao-Cortés, T. C. Walther, O. J. Gruss, and I. W. Mattaj, “GTP hydrolysis by Ran is required for nuclear envelope assembly,” <i>Molecular Cell</i>, vol. 5, no. 6. Elsevier, pp. 1013–1024, 2000.","mla":"Hetzer, Martin, et al. “GTP Hydrolysis by Ran Is Required for Nuclear Envelope Assembly.” <i>Molecular Cell</i>, vol. 5, no. 6, Elsevier, 2000, pp. 1013–24, doi:<a href=\"https://doi.org/10.1016/s1097-2765(00)80266-x\">10.1016/s1097-2765(00)80266-x</a>.","ista":"Hetzer M, Bilbao-Cortés D, Walther TC, Gruss OJ, Mattaj IW. 2000. GTP hydrolysis by Ran is required for nuclear envelope assembly. Molecular Cell. 5(6), 1013–1024.","chicago":"Hetzer, Martin, Daniel Bilbao-Cortés, Tobias C Walther, Oliver J Gruss, and Iain W Mattaj. “GTP Hydrolysis by Ran Is Required for Nuclear Envelope Assembly.” <i>Molecular Cell</i>. Elsevier, 2000. <a href=\"https://doi.org/10.1016/s1097-2765(00)80266-x\">https://doi.org/10.1016/s1097-2765(00)80266-x</a>.","short":"M. Hetzer, D. Bilbao-Cortés, T.C. Walther, O.J. Gruss, I.W. Mattaj, Molecular Cell 5 (2000) 1013–1024.","apa":"Hetzer, M., Bilbao-Cortés, D., Walther, T. C., Gruss, O. J., &#38; Mattaj, I. W. (2000). GTP hydrolysis by Ran is required for nuclear envelope assembly. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/s1097-2765(00)80266-x\">https://doi.org/10.1016/s1097-2765(00)80266-x</a>"},"keyword":["Cell Biology","Molecular Biology"],"author":[{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","first_name":"Martin W","full_name":"HETZER, Martin W"},{"full_name":"Bilbao-Cortés, Daniel","first_name":"Daniel","last_name":"Bilbao-Cortés"},{"full_name":"Walther, Tobias C","last_name":"Walther","first_name":"Tobias C"},{"first_name":"Oliver J","last_name":"Gruss","full_name":"Gruss, Oliver J"},{"last_name":"Mattaj","first_name":"Iain W","full_name":"Mattaj, Iain W"}],"_id":"11127","date_created":"2022-04-07T07:57:59Z","article_processing_charge":"No","publication_identifier":{"issn":["1097-2765"]},"page":"1013-1024","external_id":{"pmid":["10911995"]},"article_type":"original","title":"GTP hydrolysis by Ran is required for nuclear envelope assembly","volume":5,"year":"2000","publication":"Molecular Cell","day":"01","issue":"6","date_updated":"2022-07-18T08:58:31Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/S1097-2765(00)80266-X"}],"pmid":1,"doi":"10.1016/s1097-2765(00)80266-x","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_status":"published","abstract":[{"text":"Nuclear formation in Xenopus egg extracts requires cytosol and is inhibited by GTPγS, indicating a requirement for GTPase activity. Nuclear envelope (NE) vesicle fusion is extensively inhibited by GTPγS and two mutant forms of the Ran GTPase, Q69L and T24N. Depletion of either Ran or RCC1, the exchange factor for Ran, from the assembly reaction also inhibits this step of NE formation. Ran depletion can be complemented by the addition of Ran loaded with either GTP or GDP but not with GTPγS. RCC1 depletion is only complemented by RCC1 itself or by RanGTP. Thus, generation of RanGTP by RCC1 and GTP hydrolysis by Ran are both required for the extensive membrane fusion events that lead to NE formation.","lang":"eng"}],"extern":"1","date_published":"2000-06-01T00:00:00Z","status":"public"}]