[{"file":[{"success":1,"file_name":"2026_MolecularCell_Weiss.pdf","file_id":"21510","date_updated":"2026-03-30T12:04:38Z","file_size":9786677,"relation":"main_file","access_level":"open_access","date_created":"2026-03-30T12:04:38Z","checksum":"e16a7315b64a706184b177ea1621523c","creator":"dernst","content_type":"application/pdf"}],"issue":"4","publication_status":"published","OA_type":"hybrid","day":"19","_id":"21509","date_created":"2026-03-30T11:58:48Z","ddc":["570"],"oa":1,"publication":"Molecular Cell","year":"2026","publisher":"Elsevier","date_updated":"2026-03-30T12:09:08Z","title":"The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2","PlanS_conform":"1","publication_identifier":{"issn":["1097-2765"]},"citation":{"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.","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>","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>.","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>.","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.","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.","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>"},"external_id":{"pmid":["41679301"]},"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.molcel.2026.01.021","author":[{"first_name":"Joscha","last_name":"Weiss","full_name":"Weiss, Joscha"},{"full_name":"Vecchia, Luca","last_name":"Vecchia","first_name":"Luca"},{"full_name":"Domjan, David","last_name":"Domjan","first_name":"David"},{"first_name":"Simone","full_name":"Cavadini, Simone","last_name":"Cavadini"},{"full_name":"Sabantsev, Anton","last_name":"Sabantsev","first_name":"Anton"},{"full_name":"Kempf, Georg","last_name":"Kempf","first_name":"Georg"},{"full_name":"Pathare, Ganesh R.","last_name":"Pathare","first_name":"Ganesh R."},{"last_name":"Brackmann","full_name":"Brackmann, Klaus","first_name":"Klaus"},{"last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","first_name":"Alicia"},{"first_name":"Lukas","last_name":"Kater","full_name":"Kater, Lukas"},{"full_name":"Hietter-Pfeiffer, Eric","last_name":"Hietter-Pfeiffer","first_name":"Eric"},{"last_name":"Haddawi","full_name":"Haddawi, Mina","first_name":"Mina"},{"first_name":"Urja P.","full_name":"Kuber, Urja P.","last_name":"Kuber"},{"last_name":"Mühlhäusser","full_name":"Mühlhäusser, Sandra","first_name":"Sandra"},{"last_name":"Grand","full_name":"Grand, Ralph S.","first_name":"Ralph S."},{"full_name":"Stadler, Michael B.","last_name":"Stadler","first_name":"Michael B."},{"full_name":"Deindl, Sebastian","last_name":"Deindl","first_name":"Sebastian"},{"first_name":"Nicolas H.","last_name":"Thomä","full_name":"Thomä, Nicolas H."}],"status":"public","type":"journal_article","volume":86,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        86","article_type":"original","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"page":"625-639.e8","abstract":[{"lang":"eng","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."}],"file_date_updated":"2026-03-30T12:04:38Z","pmid":1,"OA_place":"publisher","has_accepted_license":"1","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).","date_published":"2026-02-19T00:00:00Z","department":[{"_id":"AlMi"}],"scopus_import":"1"},{"quality_controlled":"1","article_type":"original","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"page":"2919-2936.e12","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2025-09-24T07:54:03Z","type":"journal_article","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":85,"intvolume":"        85","has_accepted_license":"1","date_published":"2025-08-07T00:00:00Z","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.).","department":[{"_id":"AlMi"}],"scopus_import":"1","OA_place":"publisher","OA_type":"hybrid","_id":"20374","day":"07","ddc":["570"],"date_created":"2025-09-23T08:56:13Z","oa":1,"issue":"15","file":[{"access_level":"open_access","date_created":"2025-09-24T07:54:03Z","relation":"main_file","file_size":41813494,"checksum":"e60390ca629b350af3221d4718ca6534","content_type":"application/pdf","creator":"dernst","date_updated":"2025-09-24T07:54:03Z","success":1,"file_name":"2025_MolecularCell_Chakraborty.pdf","file_id":"20386"}],"publication_status":"published","citation":{"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>","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>.","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.","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>","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>.","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."},"author":[{"first_name":"Deyasini","full_name":"Chakraborty, Deyasini","last_name":"Chakraborty"},{"first_name":"Colby R.","last_name":"Sandate","full_name":"Sandate, Colby R."},{"first_name":"Luke","last_name":"Isbel","full_name":"Isbel, Luke"},{"last_name":"Kempf","full_name":"Kempf, Georg","first_name":"Georg"},{"first_name":"Joscha","last_name":"Weiss","full_name":"Weiss, Joscha"},{"first_name":"Simone","last_name":"Cavadini","full_name":"Cavadini, Simone"},{"full_name":"Kater, Lukas","last_name":"Kater","first_name":"Lukas"},{"first_name":"Jan","last_name":"Seebacher","full_name":"Seebacher, Jan"},{"last_name":"Kozicka","full_name":"Kozicka, Zuzanna","first_name":"Zuzanna"},{"full_name":"Stoos, Lisa","last_name":"Stoos","first_name":"Lisa"},{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"first_name":"Dirk","last_name":"Schübeler","full_name":"Schübeler, Dirk"},{"first_name":"Alicia","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"first_name":"Nicolas H.","full_name":"Thomä, Nicolas H.","last_name":"Thomä"}],"doi":"10.1016/j.molcel.2025.06.027","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Molecular Cell","date_updated":"2025-09-24T08:21:55Z","publisher":"Elsevier","year":"2025","publication_identifier":{"issn":["1097-2765"]},"title":"Nucleosomes specify co-factor access to p53","PlanS_conform":"1"},{"related_material":{"link":[{"url":"https://github.com/paloha/faket/","relation":"software"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":33,"intvolume":"        33","type":"journal_article","status":"public","abstract":[{"lang":"eng","text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/."}],"file_date_updated":"2025-08-05T12:15:13Z","oa_version":"Published Version","page":"820-827.e4","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","article_type":"original","quality_controlled":"1","OA_place":"publisher","pmid":1,"scopus_import":"1","department":[{"_id":"AlMi"}],"isi":1,"acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","date_published":"2025-04-03T00:00:00Z","has_accepted_license":"1","publication_status":"published","file":[{"date_updated":"2025-08-05T12:15:13Z","success":1,"file_name":"2025_Structure_Harar.pdf","file_id":"20130","file_size":4367530,"relation":"main_file","access_level":"open_access","date_created":"2025-08-05T12:15:13Z","creator":"dernst","content_type":"application/pdf","checksum":"f346bc357a66a88cca3d0eb95793fb73"}],"issue":"4","oa":1,"date_created":"2025-03-23T23:01:27Z","ddc":["570"],"day":"03","_id":"19443","OA_type":"hybrid","PlanS_conform":"1","title":"FakET: Simulating cryo-electron tomograms with neural style transfer","publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"year":"2025","corr_author":"1","date_updated":"2025-09-30T11:13:02Z","publisher":"Elsevier","publication":"Structure","month":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0001-5206-1794","first_name":"Pavol","full_name":"Harar, Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","last_name":"Harar"},{"full_name":"Herrmann, Lukas","last_name":"Herrmann","first_name":"Lukas"},{"last_name":"Grohs","full_name":"Grohs, Philipp","first_name":"Philipp"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"}],"doi":"10.1016/j.str.2025.01.020","citation":{"ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","apa":"Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>","ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.","chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.str.2025.01.020\">https://doi.org/10.1016/j.str.2025.01.020</a>.","ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4. doi:<a href=\"https://doi.org/10.1016/j.str.2025.01.020\">10.1016/j.str.2025.01.020</a>"},"external_id":{"isi":["001463196100001"],"pmid":["39947174"]}},{"date_created":"2026-01-04T23:01:33Z","oa":1,"OA_type":"gold","day":"26","_id":"20924","publication_status":"epub_ahead","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","author":[{"first_name":"Wataru","last_name":"Kobayashi","full_name":"Kobayashi, Wataru"},{"first_name":"Alicia","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"last_name":"Ruangroengkulrith","full_name":"Ruangroengkulrith, Siwat","first_name":"Siwat"},{"full_name":"Kümmecke, Maximilian","last_name":"Kümmecke","first_name":"Maximilian"},{"first_name":"Kikuë","last_name":"Tachibana","full_name":"Tachibana, Kikuë"}],"doi":"10.1016/j.xpro.2025.104295","citation":{"apa":"Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana, K. (2025). Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>","short":"W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2025).","mla":"Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>, vol. 7, 104295, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>.","ieee":"W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana, “Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination,” <i>STAR Protocols</i>, vol. 7. Elsevier, 2025.","ama":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. 2025;7. doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>","chicago":"Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>.","ista":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295."},"external_id":{"pmid":["41455105"]},"title":"Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination","PlanS_conform":"1","publication_identifier":{"eissn":["2666-1667"]},"publication":"STAR Protocols","year":"2025","corr_author":"1","publisher":"Elsevier","date_updated":"2026-01-05T11:16:11Z","oa_version":"Published Version","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2025.104295","open_access":"1"}],"abstract":[{"lang":"eng","text":"Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1"}],"article_type":"original","quality_controlled":"1","article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":7,"intvolume":"         7","status":"public","type":"journal_article","department":[{"_id":"AlMi"}],"scopus_import":"1","has_accepted_license":"1","DOAJ_listed":"1","acknowledgement":"We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).","article_number":"104295","date_published":"2025-12-26T00:00:00Z","pmid":1,"project":[{"grant_number":"101162145","name":"Circadian structural transitions of chromatin","_id":"9136c684-16d5-11f0-9cad-91c0177b365f"}],"OA_place":"publisher"},{"publication_status":"inpress","day":"19","_id":"20935","OA_type":"hybrid","oa":1,"date_created":"2026-01-04T23:01:36Z","ddc":["570"],"year":"2025","publisher":"Elsevier","date_updated":"2026-01-05T08:32:47Z","publication":"Molecular Cell","PlanS_conform":"1","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"citation":{"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>.","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.","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>","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.).","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.","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>","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>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","doi":"10.1016/j.molcel.2025.11.029","author":[{"full_name":"Kelley, Ron","last_name":"Kelley","first_name":"Ron"},{"first_name":"Sagar","last_name":"Khavnekar","full_name":"Khavnekar, Sagar"},{"first_name":"Ricardo D.","full_name":"Righetto, Ricardo D.","last_name":"Righetto"},{"first_name":"Jessica","full_name":"Heebner, Jessica","last_name":"Heebner"},{"last_name":"Obr","full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Xianjun","last_name":"Zhang","full_name":"Zhang, Xianjun"},{"last_name":"Chakraborty","full_name":"Chakraborty, Saikat","first_name":"Saikat"},{"full_name":"Tagiltsev, Grigory","last_name":"Tagiltsev","first_name":"Grigory"},{"orcid":"0000-0002-6080-839X","first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia","last_name":"Michael"},{"full_name":"Van Dorst, Sofie","last_name":"Van Dorst","first_name":"Sofie"},{"last_name":"Waltz","full_name":"Waltz, Florent","first_name":"Florent"},{"first_name":"Caitlyn L.","full_name":"Mccafferty, Caitlyn L.","last_name":"Mccafferty"},{"last_name":"Lamm","full_name":"Lamm, Lorenz","first_name":"Lorenz"},{"last_name":"Zufferey","full_name":"Zufferey, Simon","first_name":"Simon"},{"first_name":"Philippe","last_name":"Van Der Stappen","full_name":"Van Der Stappen, Philippe"},{"last_name":"Van Den Hoek","full_name":"Van Den Hoek, Hugo","first_name":"Hugo"},{"first_name":"Wojciech","full_name":"Wietrzynski, Wojciech","last_name":"Wietrzynski"},{"orcid":"0000-0001-5206-1794","first_name":"Pavol","full_name":"Harar, Pavol","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","last_name":"Harar"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"full_name":"Briggs, John A.G.","last_name":"Briggs","first_name":"John A.G."},{"last_name":"Plitzko","full_name":"Plitzko, Jürgen M.","first_name":"Jürgen M."},{"full_name":"Engel, Benjamin D.","last_name":"Engel","first_name":"Benjamin D."},{"first_name":"Abhay","full_name":"Kotecha, Abhay","last_name":"Kotecha"}],"status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","article_type":"original","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"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2025.11.029","open_access":"1"}],"OA_place":"publisher","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_published":"2025-12-19T00:00:00Z","scopus_import":"1","department":[{"_id":"AlMi"}]}]