[{"status":"public","day":"19","month":"02","OA_type":"hybrid","OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2","external_id":{"pmid":["41679301"]},"oa_version":"Published Version","PlanS_conform":"1","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"}],"_id":"21509","department":[{"_id":"AlMi"}],"date_published":"2026-02-19T00:00:00Z","pmid":1,"publication":"Molecular Cell","date_updated":"2026-03-30T12:09:08Z","quality_controlled":"1","intvolume":"        86","publication_status":"published","date_created":"2026-03-30T11:58:48Z","article_type":"original","year":"2026","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.molcel.2026.01.021","fulldoi":"https://doi.org/10.1016/j.molcel.2026.01.021","type":"journal_article","issue":"4","file_date_updated":"2026-03-30T12:04:38Z","author":[{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"last_name":"Vecchia","first_name":"Luca","full_name":"Vecchia, Luca"},{"last_name":"Domjan","full_name":"Domjan, David","first_name":"David"},{"last_name":"Cavadini","first_name":"Simone","full_name":"Cavadini, Simone"},{"last_name":"Sabantsev","full_name":"Sabantsev, Anton","first_name":"Anton"},{"last_name":"Kempf","first_name":"Georg","full_name":"Kempf, Georg"},{"last_name":"Pathare","first_name":"Ganesh R.","full_name":"Pathare, Ganesh R."},{"last_name":"Brackmann","full_name":"Brackmann, Klaus","first_name":"Klaus"},{"last_name":"Michael","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia"},{"last_name":"Kater","first_name":"Lukas","full_name":"Kater, Lukas"},{"full_name":"Hietter-Pfeiffer, Eric","first_name":"Eric","last_name":"Hietter-Pfeiffer"},{"first_name":"Mina","full_name":"Haddawi, Mina","last_name":"Haddawi"},{"last_name":"Kuber","first_name":"Urja P.","full_name":"Kuber, Urja P."},{"last_name":"Mühlhäusser","full_name":"Mühlhäusser, Sandra","first_name":"Sandra"},{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"last_name":"Stadler","full_name":"Stadler, Michael B.","first_name":"Michael B."},{"last_name":"Deindl","first_name":"Sebastian","full_name":"Deindl, Sebastian"},{"full_name":"Thomä, Nicolas H.","first_name":"Nicolas H.","last_name":"Thomä"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"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.","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.","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>.","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>.","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>"},"page":"625-639.e8","oa":1,"language":[{"iso":"eng"}],"ddc":["570"],"publisher":"Elsevier","file":[{"file_name":"2026_MolecularCell_Weiss.pdf","date_updated":"2026-03-30T12:04:38Z","file_size":9786677,"success":1,"creator":"dernst","file_id":"21510","relation":"main_file","checksum":"e16a7315b64a706184b177ea1621523c","date_created":"2026-03-30T12:04:38Z","content_type":"application/pdf","access_level":"open_access"}],"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).","volume":86,"publication_identifier":{"issn":["1097-2765"]}},{"DOAJ_listed":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"apa":"Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana, K. (2026). 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>","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, no. 1, 104295, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>.","ista":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2026. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7(1), 104295.","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, 2026. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/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, no. 1. Elsevier, 2026.","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>. 2026;7(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>","short":"W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2026)."},"file_date_updated":"2026-07-23T06:33:24Z","author":[{"last_name":"Kobayashi","full_name":"Kobayashi, Wataru","first_name":"Wataru"},{"first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","last_name":"Michael"},{"last_name":"Ruangroengkulrith","first_name":"Siwat","full_name":"Ruangroengkulrith, Siwat"},{"last_name":"Kümmecke","first_name":"Maximilian","full_name":"Kümmecke, Maximilian"},{"last_name":"Tachibana","full_name":"Tachibana, Kikuë","first_name":"Kikuë"}],"das_tickbox":"1","issue":"1","type":"journal_article","article_number":"104295","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.).","file":[{"checksum":"cf04b061a48548a649e6a2435bf120db","relation":"main_file","content_type":"application/pdf","date_created":"2026-07-23T06:33:24Z","access_level":"open_access","file_size":5531906,"file_name":"2026_StarProtocols_Kobayashi.pdf","date_updated":"2026-07-23T06:33:24Z","file_id":"22389","creator":"dernst","success":1}],"publication_identifier":{"eissn":["2666-1667"]},"volume":7,"language":[{"iso":"eng"}],"oa":1,"supplementarymaterial":"yes","publisher":"Elsevier","ddc":["570"],"researchdata_availability":"yes","external_id":{"pmid":["41455105"]},"dataavailabilitystatement":"Raw SeEN-seq data of ESRRB nucleosome binding have been deposited on the Sequence Read Achieve database under the accession PRJNA1305216. Example analysis scripts and input files for SeEN-seq analysis can be found at https://doi.org/10.5281/zenodo.17665082.","project":[{"grant_number":"101162145","_id":"9136c684-16d5-11f0-9cad-91c0177b365f","name":"Circadian structural transitions of chromatin"}],"department":[{"_id":"AlMi"}],"oa_version":"Published Version","PlanS_conform":"1","abstract":[{"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","lang":"eng"}],"_id":"20924","status":"public","day":"20","month":"03","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination","OA_type":"gold","has_accepted_license":"1","OA_place":"publisher","year":"2026","date_created":"2026-01-04T23:01:33Z","publication_status":"published","article_type":"original","doi":"10.1016/j.xpro.2025.104295","fulldoi":"https://doi.org/10.1016/j.xpro.2025.104295","article_processing_charge":"Yes","scopus_import":"1","pmid":1,"publication":"STAR Protocols","date_published":"2026-03-20T00:00:00Z","intvolume":"         7","quality_controlled":"1","date_updated":"2026-07-23T06:34:37Z"},{"page":"213-230.e7","language":[{"iso":"eng"}],"oa":1,"ddc":["570"],"researchdata_availability":"yes","publisher":"Elsevier","supplementarymaterial":"yes","file":[{"checksum":"96a2f8519124d1a0d9de8d2594bf7147","relation":"main_file","date_created":"2026-07-28T07:38:45Z","content_type":"application/pdf","access_level":"open_access","file_size":26749637,"date_updated":"2026-07-28T07:38:45Z","file_name":"2026_MolecularCell_Kelley.pdf","file_id":"22599","creator":"dernst","success":1}],"acknowledgement":"Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.","volume":86,"publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"das_tickbox":"1","type":"journal_article","issue":"1","file_date_updated":"2026-07-28T07:38:45Z","author":[{"last_name":"Kelley","first_name":"Ron","full_name":"Kelley, Ron"},{"full_name":"Khavnekar, Sagar","first_name":"Sagar","last_name":"Khavnekar"},{"first_name":"Ricardo D.","full_name":"Righetto, Ricardo D.","last_name":"Righetto"},{"last_name":"Heebner","full_name":"Heebner, Jessica","first_name":"Jessica"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","first_name":"Martin","last_name":"Obr"},{"first_name":"Xianjun","full_name":"Zhang, Xianjun","last_name":"Zhang"},{"last_name":"Chakraborty","first_name":"Saikat","full_name":"Chakraborty, Saikat"},{"last_name":"Tagiltsev","first_name":"Grigory","full_name":"Tagiltsev, Grigory"},{"last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","first_name":"Alicia"},{"full_name":"Van Dorst, Sofie","first_name":"Sofie","last_name":"Van Dorst"},{"last_name":"Waltz","first_name":"Florent","full_name":"Waltz, Florent"},{"first_name":"Caitlyn L.","full_name":"Mccafferty, Caitlyn L.","last_name":"Mccafferty"},{"last_name":"Lamm","first_name":"Lorenz","full_name":"Lamm, Lorenz"},{"full_name":"Zufferey, Simon","first_name":"Simon","last_name":"Zufferey"},{"last_name":"Van Der Stappen","full_name":"Van Der Stappen, Philippe","first_name":"Philippe"},{"first_name":"Hugo","full_name":"Van Den Hoek, Hugo","last_name":"Van Den Hoek"},{"full_name":"Wietrzynski, Wojciech","first_name":"Wojciech","last_name":"Wietrzynski"},{"first_name":"Pavol","full_name":"Harar, Pavol","orcid":"0000-0001-5206-1794","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5","last_name":"Harar"},{"full_name":"Wan, William","first_name":"William","last_name":"Wan"},{"last_name":"Briggs","first_name":"John A.G.","full_name":"Briggs, John A.G."},{"last_name":"Plitzko","first_name":"Jürgen M.","full_name":"Plitzko, Jürgen M."},{"last_name":"Engel","first_name":"Benjamin D.","full_name":"Engel, Benjamin D."},{"full_name":"Kotecha, Abhay","first_name":"Abhay","last_name":"Kotecha"}],"citation":{"ista":"Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. 2026. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 86(1), 213–230.e7.","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>, vol. 86, no. 1, Elsevier, 2026, p. 213–230.e7, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>.","apa":"Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (2026). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>","chicago":"Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>.","ieee":"R. Kelley <i>et al.</i>, “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” <i>Molecular Cell</i>, vol. 86, no. 1. Elsevier, p. 213–230.e7, 2026.","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>. 2026;86(1):213-230.e7. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>","short":"R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell 86 (2026) 213–230.e7."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2026-01-08T00:00:00Z","publication":"Molecular Cell","quality_controlled":"1","date_updated":"2026-07-28T07:39:23Z","intvolume":"        86","date_created":"2026-01-04T23:01:36Z","article_type":"original","publication_status":"published","year":"2026","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.molcel.2025.11.029","fulldoi":"https://doi.org/10.1016/j.molcel.2025.11.029","status":"public","month":"01","day":"08","OA_place":"publisher","OA_type":"hybrid","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","dataavailabilitystatement":"Raw EM data are available at the EMPIAR under accession code EMPIAR: EMPIAR-11830. Annotation and processing information for all 1,829 tomograms are provided in spreadsheet format.153 The following subtomogram averages have been deposited at the Electron Microscopy Data Bank (EMDB): 80S ribosome (EMDB: EMD-51847), nucleosome (EMDB: EMD-19906), PSII (EMDB: EMD-51731), Rubisco (EMDB: EMD-51848), microtubule (EMDB: EMD-51804), clathrin (EMDB: EMD-51789), and ATP synthase (EMDB: EMD-51802). Segmentations shown in Figures 2 and 3 are deposited on Zenodo (https://doi.org/10.5281/zenodo.15875785). Particle positions and orientations used for STA, along with all resources derived from this work, are available on GitHub (https://github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations). Reconstructed tomograms and annotations are also available to explore interactively at the CZII Cryo-ET Data Portal (DS-10302, https://cryoetdataportal.czscience.com/datasets/10302/). Raw data for cryo-PFIB/SEM slice-and-view of a whole C. reinhardtii cell has also been deposited (EMPIAR: EMPIAR-11275).\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","oa_version":"Published Version","PlanS_conform":"1","abstract":[{"lang":"eng","text":"In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics."}],"_id":"20935","department":[{"_id":"AlMi"}]},{"main_file_link":[{"url":"https://doi.org/10.1038/s41556-026-02041-4","open_access":"1"}],"das_tickbox":"1","type":"journal_article","author":[{"full_name":"Aygenli, Fatih","first_name":"Fatih","last_name":"Aygenli"},{"last_name":"Huschet","full_name":"Huschet, Lukas A.","first_name":"Lukas A."},{"last_name":"Popp","first_name":"Tanja","full_name":"Popp, Tanja"},{"last_name":"Ribeiro","first_name":"Andrea","full_name":"Ribeiro, Andrea"},{"id":"db547c8c-329f-11ee-a353-cde802618f9e","orcid":"0000-0002-0062-2817","full_name":"Barkhatova, Darina","first_name":"Darina","last_name":"Barkhatova"},{"first_name":"Céline","full_name":"Jouffe, Céline","last_name":"Jouffe"},{"last_name":"Trozzo","first_name":"Ricardo","full_name":"Trozzo, Ricardo"},{"full_name":"Menet, Jerome S.","first_name":"Jerome S.","last_name":"Menet"},{"last_name":"Rad","first_name":"Roland","full_name":"Rad, Roland"},{"full_name":"Dyar, Kenneth A.","first_name":"Kenneth A.","last_name":"Dyar"},{"last_name":"Lech","full_name":"Lech, Maciej","first_name":"Maciej"},{"first_name":"Tobias","full_name":"Straub, Tobias","last_name":"Straub"},{"first_name":"Alicia","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Robles, Maria S.","first_name":"Maria S.","last_name":"Robles"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ama":"Aygenli F, Huschet LA, Popp T, et al. CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators. <i>Nature Cell Biology</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41556-026-02041-4\">10.1038/s41556-026-02041-4</a>","ieee":"F. Aygenli <i>et al.</i>, “CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators,” <i>Nature Cell Biology</i>. Springer Nature, 2026.","short":"F. Aygenli, L.A. Huschet, T. Popp, A. Ribeiro, D. Barkhatova, C. Jouffe, R. Trozzo, J.S. Menet, R. Rad, K.A. Dyar, M. Lech, T. Straub, A.K. Michael, M.S. Robles, Nature Cell Biology (2026).","apa":"Aygenli, F., Huschet, L. A., Popp, T., Ribeiro, A., Barkhatova, D., Jouffe, C., … Robles, M. S. (2026). CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-026-02041-4\">https://doi.org/10.1038/s41556-026-02041-4</a>","ista":"Aygenli F, Huschet LA, Popp T, Ribeiro A, Barkhatova D, Jouffe C, Trozzo R, Menet JS, Rad R, Dyar KA, Lech M, Straub T, Michael AK, Robles MS. 2026. CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators. Nature Cell Biology.","mla":"Aygenli, Fatih, et al. “CLOCK/BMAL1 Interactome Uncovers Homeodomain Factors as Tissue Regulators.” <i>Nature Cell Biology</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41556-026-02041-4\">10.1038/s41556-026-02041-4</a>.","chicago":"Aygenli, Fatih, Lukas A. Huschet, Tanja Popp, Andrea Ribeiro, Darina Barkhatova, Céline Jouffe, Ricardo Trozzo, et al. “CLOCK/BMAL1 Interactome Uncovers Homeodomain Factors as Tissue Regulators.” <i>Nature Cell Biology</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41556-026-02041-4\">https://doi.org/10.1038/s41556-026-02041-4</a>."},"ddc":["570"],"researchdata_availability":"yes","publisher":"Springer Nature","supplementarymaterial":"yes","oa":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"acknowledgement":"We thank all members of the Robles’ group for critical comments on and edits to this paper. We thank S. Kay for providing dihXY HCC cell lines and D. Firsov and Y. Bignon for mouse BMAL1-knockout (KO) kidney tissues. This work was supported by the German Research Foundation (DFG) project no. 213249687—SFB 1064 and RO 5675/1-1 to M.S.R., F.A. and L.A.H. M.S.R was also supported by DFG INST 86/1800-1 FUGG and LMU Munich’s Institutional Strategy LMU excellent within the framework of the German Excellence Initiative. J.S.M. was supported by US National Institutes of Health grant nos. R01GM145737 and R01DK128133. A.K.M. was supported by an ERC grant ‘ChromaChrono’ 101162145. Open access funding provided by Ludwig-Maximilians-Universität München.","OA_type":"hybrid","OA_place":"publisher","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators","status":"public","day":"06","month":"08","PlanS_conform":"1","oa_version":"Published Version","_id":"22720","abstract":[{"text":"Circadian clocks underlie daily rhythms in physiology by coordinating temporal patterns of gene expression and protein function throughout the body. At the core of this system in mammals is CLOCK/BMAL1, a ubiquitously expressed heterodimeric transcription factor complex that orchestrates tissue-specific circadian gene expression. The basis for this specificity remains unclear, but tissue-specific interactions at chromatin could provide one. Here we used chromatin immunoprecipitation coupled to mass spectrometry to map CLOCK/BMAL1-associated protein complexes on chromatin in mouse liver, kidney and lung. We detected 1,510 associated proteins, most of which were tissue-specific and not explained by protein abundance. Among these, we identified the homeodomain transcription factors PROX1, HNF1B and HOXA5 as tissue-enriched interactors that bind BMAL1, co-occupy most BMAL1 genomic sites and establish organ-restricted circadian transcription. Our findings demonstrate that tissue-specific transcription factors confer cellular identity on the core clock, thereby contributing to organ-specific patterns of rhythmic gene expression.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"AlMi"}],"project":[{"name":"Circadian structural transitions of chromatin","_id":"9136c684-16d5-11f0-9cad-91c0177b365f","grant_number":"101162145"}],"dataavailabilitystatement":"Proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE64 partner repository with the dataset identifiers PXD062751 and PXD077567. RNA-seq data are available in the European Nucleotide Archive (ENA) under accession no. PRJEB93884, and ChIP–seq data at the Gene Expression Omnibus (GEO) under accession no. GSE302237. AlphaFold 3 interaction prediction parameters can be provided during the revision process on editorial and/or review request. Source data are provided with this paper.","external_id":{"pmid":["42562924"]},"date_updated":"2026-08-18T08:03:22Z","quality_controlled":"1","date_published":"2026-08-06T00:00:00Z","pmid":1,"publication":"Nature Cell Biology","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","doi":"10.1038/s41556-026-02041-4","fulldoi":"https://doi.org/10.1038/s41556-026-02041-4","article_type":"original","date_created":"2026-08-16T22:01:44Z","publication_status":"epub_ahead","year":"2026"},{"author":[{"full_name":"Chakraborty, Deyasini","first_name":"Deyasini","last_name":"Chakraborty"},{"last_name":"Sandate","full_name":"Sandate, Colby R.","first_name":"Colby R."},{"first_name":"Luke","full_name":"Isbel, Luke","last_name":"Isbel"},{"first_name":"Georg","full_name":"Kempf, Georg","last_name":"Kempf"},{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"first_name":"Simone","full_name":"Cavadini, Simone","last_name":"Cavadini"},{"full_name":"Kater, Lukas","first_name":"Lukas","last_name":"Kater"},{"full_name":"Seebacher, Jan","first_name":"Jan","last_name":"Seebacher"},{"last_name":"Kozicka","full_name":"Kozicka, Zuzanna","first_name":"Zuzanna"},{"last_name":"Stoos","first_name":"Lisa","full_name":"Stoos, Lisa"},{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"full_name":"Schübeler, Dirk","first_name":"Dirk","last_name":"Schübeler"},{"orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","last_name":"Michael"},{"first_name":"Nicolas H.","full_name":"Thomä, Nicolas H.","last_name":"Thomä"}],"file_date_updated":"2025-09-24T07:54:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"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>.","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>.","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.","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>"},"type":"journal_article","issue":"15","volume":85,"publication_identifier":{"issn":["1097-2765"]},"file":[{"relation":"main_file","checksum":"e60390ca629b350af3221d4718ca6534","content_type":"application/pdf","access_level":"open_access","date_created":"2025-09-24T07:54:03Z","file_name":"2025_MolecularCell_Chakraborty.pdf","date_updated":"2025-09-24T07:54:03Z","file_size":41813494,"success":1,"file_id":"20386","creator":"dernst"}],"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.).","ddc":["570"],"publisher":"Elsevier","page":"2919-2936.e12","oa":1,"language":[{"iso":"eng"}],"_id":"20374","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."}],"PlanS_conform":"1","oa_version":"Published Version","department":[{"_id":"AlMi"}],"OA_place":"publisher","OA_type":"hybrid","has_accepted_license":"1","title":"Nucleosomes specify co-factor access to p53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","month":"08","status":"public","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.molcel.2025.06.027","doi":"10.1016/j.molcel.2025.06.027","date_created":"2025-09-23T08:56:13Z","publication_status":"published","article_type":"original","year":"2025","quality_controlled":"1","date_updated":"2025-09-24T08:21:55Z","intvolume":"        85","date_published":"2025-08-07T00:00:00Z","publication":"Molecular Cell"},{"main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06282-3","open_access":"1"}],"type":"journal_article","issue":"7969","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","first_name":"Alicia","last_name":"Michael"},{"first_name":"Lisa","full_name":"Stoos, Lisa","last_name":"Stoos"},{"first_name":"Priya","full_name":"Crosby, Priya","last_name":"Crosby"},{"first_name":"Nikolas","full_name":"Eggers, Nikolas","last_name":"Eggers"},{"first_name":"Xinyu Y.","full_name":"Nie, Xinyu Y.","last_name":"Nie"},{"last_name":"Makasheva","full_name":"Makasheva, Kristina","first_name":"Kristina"},{"full_name":"Minnich, Martina","first_name":"Martina","last_name":"Minnich"},{"full_name":"Healy, Kelly L.","first_name":"Kelly L.","last_name":"Healy"},{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"first_name":"Georg","full_name":"Kempf, Georg","last_name":"Kempf"},{"last_name":"Cavadini","full_name":"Cavadini, Simone","first_name":"Simone"},{"full_name":"Kater, Lukas","first_name":"Lukas","last_name":"Kater"},{"last_name":"Seebacher","first_name":"Jan","full_name":"Seebacher, Jan"},{"last_name":"Vecchia","first_name":"Luca","full_name":"Vecchia, Luca"},{"full_name":"Chakraborty, Deyasini","first_name":"Deyasini","last_name":"Chakraborty"},{"full_name":"Isbel, Luke","first_name":"Luke","last_name":"Isbel"},{"last_name":"Grand","first_name":"Ralph S.","full_name":"Grand, Ralph S."},{"last_name":"Andersch","full_name":"Andersch, Florian","first_name":"Florian"},{"full_name":"Fribourgh, Jennifer L.","first_name":"Jennifer L.","last_name":"Fribourgh"},{"full_name":"Schübeler, Dirk","first_name":"Dirk","last_name":"Schübeler"},{"last_name":"Zuber","full_name":"Zuber, Johannes","first_name":"Johannes"},{"last_name":"Liu","first_name":"Andrew C.","full_name":"Liu, Andrew C."},{"last_name":"Becker","full_name":"Becker, Peter B.","first_name":"Peter B."},{"last_name":"Fierz","full_name":"Fierz, Beat","first_name":"Beat"},{"last_name":"Partch","first_name":"Carrie L.","full_name":"Partch, Carrie L."},{"full_name":"Menet, Jerome S.","first_name":"Jerome S.","last_name":"Menet"},{"first_name":"Nicolas H.","full_name":"Thomä, Nicolas H.","last_name":"Thomä"}],"citation":{"apa":"Michael, A. K., Stoos, L., Crosby, P., Eggers, N., Nie, X. Y., Makasheva, K., … Thomä, N. H. (2023). Cooperation between bHLH transcription factors and histones for DNA access. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06282-3\">https://doi.org/10.1038/s41586-023-06282-3</a>","ista":"Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH. 2023. Cooperation between bHLH transcription factors and histones for DNA access. Nature. 619(7969), 385–393.","mla":"Michael, Alicia K., et al. “Cooperation between BHLH Transcription Factors and Histones for DNA Access.” <i>Nature</i>, vol. 619, no. 7969, Springer Nature, 2023, pp. 385–93, doi:<a href=\"https://doi.org/10.1038/s41586-023-06282-3\">10.1038/s41586-023-06282-3</a>.","chicago":"Michael, Alicia K., Lisa Stoos, Priya Crosby, Nikolas Eggers, Xinyu Y. Nie, Kristina Makasheva, Martina Minnich, et al. “Cooperation between BHLH Transcription Factors and Histones for DNA Access.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06282-3\">https://doi.org/10.1038/s41586-023-06282-3</a>.","ama":"Michael AK, Stoos L, Crosby P, et al. Cooperation between bHLH transcription factors and histones for DNA access. <i>Nature</i>. 2023;619(7969):385-393. doi:<a href=\"https://doi.org/10.1038/s41586-023-06282-3\">10.1038/s41586-023-06282-3</a>","ieee":"A. K. Michael <i>et al.</i>, “Cooperation between bHLH transcription factors and histones for DNA access,” <i>Nature</i>, vol. 619, no. 7969. Springer Nature, pp. 385–393, 2023.","short":"A.K. Michael, L. Stoos, P. Crosby, N. Eggers, X.Y. Nie, K. Makasheva, M. Minnich, K.L. Healy, J. Weiss, G. Kempf, S. Cavadini, L. Kater, J. Seebacher, L. Vecchia, D. Chakraborty, L. Isbel, R.S. Grand, F. Andersch, J.L. Fribourgh, D. Schübeler, J. Zuber, A.C. Liu, P.B. Becker, B. Fierz, C.L. Partch, J.S. Menet, N.H. Thomä, Nature 619 (2023) 385–393."},"page":"385-393","oa":1,"language":[{"iso":"eng"}],"publisher":"Springer Nature","volume":619,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"07","day":"05","status":"public","extern":"1","title":"Cooperation between bHLH transcription factors and histones for DNA access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members<jats:sup>1</jats:sup>. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. <jats:sup>2,3</jats:sup>). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry–exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A–H2B acidic patch<jats:sup>4</jats:sup>, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes<jats:sup>5–7</jats:sup> at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors."}],"_id":"15148","oa_version":"Published Version","date_published":"2023-07-05T00:00:00Z","publication":"Nature","date_updated":"2024-03-25T12:42:29Z","quality_controlled":"1","intvolume":"       619","date_created":"2024-03-21T07:52:44Z","publication_status":"published","article_type":"original","year":"2023","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41586-023-06282-3","doi":"10.1038/s41586-023-06282-3"},{"external_id":{"pmid":["37386214"]},"_id":"15149","abstract":[{"text":"The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.","lang":"eng"}],"oa_version":"Published Version","keyword":["Molecular Biology","Structural Biology"],"month":"06","day":"29","status":"public","extern":"1","title":"Readout of histone methylation by Trim24 locally restricts chromatin opening by p53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_created":"2024-03-21T07:53:24Z","publication_status":"published","year":"2023","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/s41594-023-01021-8","doi":"10.1038/s41594-023-01021-8","date_published":"2023-06-29T00:00:00Z","publication":"Nature Structural & Molecular Biology","pmid":1,"date_updated":"2024-03-25T12:37:20Z","quality_controlled":"1","intvolume":"        30","author":[{"last_name":"Isbel","first_name":"Luke","full_name":"Isbel, Luke"},{"first_name":"Murat","full_name":"Iskar, Murat","last_name":"Iskar"},{"last_name":"Durdu","first_name":"Sevi","full_name":"Durdu, Sevi"},{"last_name":"Weiss","full_name":"Weiss, Joscha","first_name":"Joscha"},{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"last_name":"Hietter-Pfeiffer","full_name":"Hietter-Pfeiffer, Eric","first_name":"Eric"},{"last_name":"Kozicka","first_name":"Zuzanna","full_name":"Kozicka, Zuzanna"},{"orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","last_name":"Michael"},{"last_name":"Burger","full_name":"Burger, Lukas","first_name":"Lukas"},{"last_name":"Thomä","first_name":"Nicolas H.","full_name":"Thomä, Nicolas H."},{"last_name":"Schübeler","first_name":"Dirk","full_name":"Schübeler, Dirk"}],"citation":{"ieee":"L. Isbel <i>et al.</i>, “Readout of histone methylation by Trim24 locally restricts chromatin opening by p53,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 30, no. 7. Springer Nature, pp. 948–957, 2023.","ama":"Isbel L, Iskar M, Durdu S, et al. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. <i>Nature Structural &#38; Molecular Biology</i>. 2023;30(7):948-957. doi:<a href=\"https://doi.org/10.1038/s41594-023-01021-8\">10.1038/s41594-023-01021-8</a>","short":"L. Isbel, M. Iskar, S. Durdu, J. Weiss, R.S. Grand, E. Hietter-Pfeiffer, Z. Kozicka, A.K. Michael, L. Burger, N.H. Thomä, D. Schübeler, Nature Structural &#38; Molecular Biology 30 (2023) 948–957.","apa":"Isbel, L., Iskar, M., Durdu, S., Weiss, J., Grand, R. S., Hietter-Pfeiffer, E., … Schübeler, D. (2023). Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01021-8\">https://doi.org/10.1038/s41594-023-01021-8</a>","ista":"Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D. 2023. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural &#38; Molecular Biology. 30(7), 948–957.","mla":"Isbel, Luke, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 30, no. 7, Springer Nature, 2023, pp. 948–57, doi:<a href=\"https://doi.org/10.1038/s41594-023-01021-8\">10.1038/s41594-023-01021-8</a>.","chicago":"Isbel, Luke, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S. Grand, Eric Hietter-Pfeiffer, Zuzanna Kozicka, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41594-023-01021-8\">https://doi.org/10.1038/s41594-023-01021-8</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-023-01021-8"}],"type":"journal_article","issue":"7","volume":30,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"page":"948-957","language":[{"iso":"eng"}],"oa":1,"publisher":"Springer Nature"},{"page":"133-137","date_published":"2021-08-05T00:00:00Z","publication":"Nature","language":[{"iso":"eng"}],"date_updated":"2024-03-25T12:34:31Z","quality_controlled":"1","publisher":"Springer Nature","intvolume":"       596","publication_status":"published","article_type":"original","date_created":"2024-03-21T07:53:48Z","year":"2021","scopus_import":"1","article_processing_charge":"No","volume":596,"fulldoi":"https://doi.org/10.1038/s41586-021-03689-8","doi":"10.1038/s41586-021-03689-8","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"day":"05","month":"08","status":"public","extern":"1","title":"BANP opens chromatin and activates CpG-island-regulated genes","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15150","abstract":[{"text":"The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3,4,5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6,7,8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.","lang":"eng"}],"author":[{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"last_name":"Burger","full_name":"Burger, Lukas","first_name":"Lukas"},{"last_name":"Gräwe","first_name":"Cathrin","full_name":"Gräwe, Cathrin"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","first_name":"Alicia","last_name":"Michael"},{"first_name":"Luke","full_name":"Isbel, Luke","last_name":"Isbel"},{"full_name":"Hess, Daniel","first_name":"Daniel","last_name":"Hess"},{"full_name":"Hoerner, Leslie","first_name":"Leslie","last_name":"Hoerner"},{"last_name":"Iesmantavicius","full_name":"Iesmantavicius, Vytautas","first_name":"Vytautas"},{"first_name":"Sevi","full_name":"Durdu, Sevi","last_name":"Durdu"},{"first_name":"Marco","full_name":"Pregnolato, Marco","last_name":"Pregnolato"},{"last_name":"Krebs","full_name":"Krebs, Arnaud R.","first_name":"Arnaud R."},{"full_name":"Smallwood, Sébastien A.","first_name":"Sébastien A.","last_name":"Smallwood"},{"last_name":"Thomä","first_name":"Nicolas","full_name":"Thomä, Nicolas"},{"last_name":"Vermeulen","first_name":"Michiel","full_name":"Vermeulen, Michiel"},{"last_name":"Schübeler","first_name":"Dirk","full_name":"Schübeler, Dirk"}],"oa_version":"None","citation":{"chicago":"Grand, Ralph S., Lukas Burger, Cathrin Gräwe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03689-8\">https://doi.org/10.1038/s41586-021-03689-8</a>.","mla":"Grand, Ralph S., et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” <i>Nature</i>, vol. 596, Springer Nature, 2021, pp. 133–37, doi:<a href=\"https://doi.org/10.1038/s41586-021-03689-8\">10.1038/s41586-021-03689-8</a>.","ista":"Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. 2021. BANP opens chromatin and activates CpG-island-regulated genes. Nature. 596, 133–137.","apa":"Grand, R. S., Burger, L., Gräwe, C., Michael, A. K., Isbel, L., Hess, D., … Schübeler, D. (2021). BANP opens chromatin and activates CpG-island-regulated genes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03689-8\">https://doi.org/10.1038/s41586-021-03689-8</a>","short":"R.S. Grand, L. Burger, C. Gräwe, A.K. Michael, L. Isbel, D. Hess, L. Hoerner, V. Iesmantavicius, S. Durdu, M. Pregnolato, A.R. Krebs, S.A. Smallwood, N. Thomä, M. Vermeulen, D. Schübeler, Nature 596 (2021) 133–137.","ieee":"R. S. Grand <i>et al.</i>, “BANP opens chromatin and activates CpG-island-regulated genes,” <i>Nature</i>, vol. 596. Springer Nature, pp. 133–137, 2021.","ama":"Grand RS, Burger L, Gräwe C, et al. BANP opens chromatin and activates CpG-island-regulated genes. <i>Nature</i>. 2021;596:133-137. doi:<a href=\"https://doi.org/10.1038/s41586-021-03689-8\">10.1038/s41586-021-03689-8</a>"}},{"citation":{"ieee":"A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” <i>Cell</i>, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021.","ama":"Michael AK, Thomä NH. Reading the chromatinized genome. <i>Cell</i>. 2021;184(14):3599-3611. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">10.1016/j.cell.2021.05.029</a>","short":"A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.","apa":"Michael, A. K., &#38; Thomä, N. H. (2021). Reading the chromatinized genome. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">https://doi.org/10.1016/j.cell.2021.05.029</a>","mla":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” <i>Cell</i>, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">10.1016/j.cell.2021.05.029</a>.","ista":"Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611.","chicago":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">https://doi.org/10.1016/j.cell.2021.05.029</a>."},"author":[{"first_name":"Alicia","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"first_name":"Nicolas H.","full_name":"Thomä, Nicolas H.","last_name":"Thomä"}],"type":"journal_article","issue":"14","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2021.05.029"}],"publication_identifier":{"issn":["0092-8674"]},"volume":184,"publisher":"Elsevier","oa":1,"language":[{"iso":"eng"}],"page":"3599-3611","_id":"15151","abstract":[{"text":"Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair.","lang":"eng"}],"oa_version":"Published Version","title":"Reading the chromatinized genome","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","day":"08","month":"07","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"fulldoi":"https://doi.org/10.1016/j.cell.2021.05.029","doi":"10.1016/j.cell.2021.05.029","scopus_import":"1","article_processing_charge":"No","year":"2021","date_created":"2024-03-21T07:54:19Z","publication_status":"published","article_type":"review","intvolume":"       184","quality_controlled":"1","date_updated":"2024-03-25T12:31:39Z","publication":"Cell","date_published":"2021-07-08T00:00:00Z"},{"page":"1460-1465","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science ","volume":368,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"issue":"6498","type":"journal_article","author":[{"last_name":"Michael","orcid":"0000-0002-6080-839X","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen"},{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"last_name":"Isbel","first_name":"Luke","full_name":"Isbel, Luke"},{"last_name":"Cavadini","full_name":"Cavadini, Simone","first_name":"Simone"},{"first_name":"Zuzanna","full_name":"Kozicka, Zuzanna","last_name":"Kozicka"},{"last_name":"Kempf","full_name":"Kempf, Georg","first_name":"Georg"},{"full_name":"Bunker, Richard D.","first_name":"Richard D.","last_name":"Bunker"},{"last_name":"Schenk","first_name":"Andreas D.","full_name":"Schenk, Andreas D."},{"last_name":"Graff-Meyer","full_name":"Graff-Meyer, Alexandra","first_name":"Alexandra"},{"last_name":"Pathare","first_name":"Ganesh R.","full_name":"Pathare, Ganesh R."},{"full_name":"Weiss, Joscha","first_name":"Joscha","last_name":"Weiss"},{"first_name":"Syota","full_name":"Matsumoto, Syota","last_name":"Matsumoto"},{"last_name":"Burger","first_name":"Lukas","full_name":"Burger, Lukas"},{"first_name":"Dirk","full_name":"Schübeler, Dirk","last_name":"Schübeler"},{"last_name":"Thomä","full_name":"Thomä, Nicolas H.","first_name":"Nicolas H."}],"citation":{"short":"A.K. Michael, R.S. Grand, L. Isbel, S. Cavadini, Z. Kozicka, G. Kempf, R.D. Bunker, A.D. Schenk, A. Graff-Meyer, G.R. Pathare, J. Weiss, S. Matsumoto, L. Burger, D. Schübeler, N.H. Thomä, Science 368 (2020) 1460–1465.","ieee":"A. K. Michael <i>et al.</i>, “Mechanisms of OCT4-SOX2 motif readout on nucleosomes,” <i>Science</i>, vol. 368, no. 6498. American Association for the Advancement of Science , pp. 1460–1465, 2020.","ama":"Michael AK, Grand RS, Isbel L, et al. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. <i>Science</i>. 2020;368(6498):1460-1465. doi:<a href=\"https://doi.org/10.1126/science.abb0074\">10.1126/science.abb0074</a>","chicago":"Michael, Alicia K., Ralph S. Grand, Luke Isbel, Simone Cavadini, Zuzanna Kozicka, Georg Kempf, Richard D. Bunker, et al. “Mechanisms of OCT4-SOX2 Motif Readout on Nucleosomes.” <i>Science</i>. American Association for the Advancement of Science , 2020. <a href=\"https://doi.org/10.1126/science.abb0074\">https://doi.org/10.1126/science.abb0074</a>.","apa":"Michael, A. K., Grand, R. S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., … Thomä, N. H. (2020). Mechanisms of OCT4-SOX2 motif readout on nucleosomes. <i>Science</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/science.abb0074\">https://doi.org/10.1126/science.abb0074</a>","ista":"Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. 2020. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science. 368(6498), 1460–1465.","mla":"Michael, Alicia K., et al. “Mechanisms of OCT4-SOX2 Motif Readout on Nucleosomes.” <i>Science</i>, vol. 368, no. 6498, American Association for the Advancement of Science , 2020, pp. 1460–65, doi:<a href=\"https://doi.org/10.1126/science.abb0074\">10.1126/science.abb0074</a>."},"date_published":"2020-04-23T00:00:00Z","publication":"Science","quality_controlled":"1","date_updated":"2024-03-25T12:29:34Z","intvolume":"       368","publication_status":"published","date_created":"2024-03-21T07:54:44Z","article_type":"original","year":"2020","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1126/science.abb0074","doi":"10.1126/science.abb0074","day":"23","month":"04","status":"public","extern":"1","title":"Mechanisms of OCT4-SOX2 motif readout on nucleosomes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo–electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.","lang":"eng"}],"_id":"15152","oa_version":"None"},{"day":"26","month":"02","status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"title":"Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","_id":"15153","abstract":[{"lang":"eng","text":"Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1."}],"oa_version":"Published Version","publication":"eLife","date_published":"2020-02-26T00:00:00Z","intvolume":"         9","quality_controlled":"1","date_updated":"2024-03-25T12:25:02Z","year":"2020","date_created":"2024-03-21T07:55:12Z","article_type":"original","publication_status":"published","fulldoi":"https://doi.org/10.7554/elife.55275","doi":"10.7554/elife.55275","article_processing_charge":"No","scopus_import":"1","type":"journal_article","article_number":"55275","main_file_link":[{"url":"https://doi.org/10.7554/eLife.55275","open_access":"1"}],"citation":{"short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).","ieee":"J. L. Fribourgh <i>et al.</i>, “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>","chicago":"Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55275\">https://doi.org/10.7554/elife.55275</a>","mla":"Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” <i>ELife</i>, vol. 9, 55275, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55275\">10.7554/elife.55275</a>.","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275."},"author":[{"full_name":"Fribourgh, Jennifer L","first_name":"Jennifer L","last_name":"Fribourgh"},{"last_name":"Srivastava","first_name":"Ashutosh","full_name":"Srivastava, Ashutosh"},{"full_name":"Sandate, Colby R","first_name":"Colby R","last_name":"Sandate"},{"last_name":"Michael","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"last_name":"Hsu","full_name":"Hsu, Peter L","first_name":"Peter L"},{"last_name":"Rakers","first_name":"Christin","full_name":"Rakers, Christin"},{"first_name":"Leslee T","full_name":"Nguyen, Leslee T","last_name":"Nguyen"},{"last_name":"Torgrimson","full_name":"Torgrimson, Megan R","first_name":"Megan R"},{"last_name":"Parico","full_name":"Parico, Gian Carlo G","first_name":"Gian Carlo G"},{"first_name":"Sarvind","full_name":"Tripathi, Sarvind","last_name":"Tripathi"},{"last_name":"Zheng","first_name":"Ning","full_name":"Zheng, Ning"},{"full_name":"Lander, Gabriel C","first_name":"Gabriel C","last_name":"Lander"},{"last_name":"Hirota","full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi"},{"first_name":"Florence","full_name":"Tama, Florence","last_name":"Tama"},{"first_name":"Carrie L","full_name":"Partch, Carrie L","last_name":"Partch"}],"language":[{"iso":"eng"}],"oa":1,"publisher":"eLife Sciences Publications","publication_identifier":{"issn":["2050-084X"]},"volume":9},{"citation":{"chicago":"Fribourgh, Jennifer L., Ashutosh Srivastava, Colby R. Sandate, Alicia K. Michael, Peter L. Hsu, Christin Rakers, Leslee T. Nguyen, et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” <i>BioRxiv</i>, 2019. <a href=\"https://doi.org/10.1101/740464\">https://doi.org/10.1101/740464</a>.","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2019. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv, <a href=\"https://doi.org/10.1101/740464\">10.1101/740464</a>.","mla":"Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” <i>BioRxiv</i>, 2019, doi:<a href=\"https://doi.org/10.1101/740464\">10.1101/740464</a>.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2019). Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/740464\">https://doi.org/10.1101/740464</a>","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, BioRxiv (2019).","ieee":"J. L. Fribourgh <i>et al.</i>, “Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms,” <i>bioRxiv</i>. 2019.","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. <i>bioRxiv</i>. 2019. doi:<a href=\"https://doi.org/10.1101/740464\">10.1101/740464</a>"},"author":[{"last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L.","first_name":"Jennifer L."},{"last_name":"Srivastava","full_name":"Srivastava, Ashutosh","first_name":"Ashutosh"},{"last_name":"Sandate","first_name":"Colby R.","full_name":"Sandate, Colby R."},{"last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","first_name":"Alicia"},{"last_name":"Hsu","first_name":"Peter L.","full_name":"Hsu, Peter L."},{"first_name":"Christin","full_name":"Rakers, Christin","last_name":"Rakers"},{"full_name":"Nguyen, Leslee T.","first_name":"Leslee T.","last_name":"Nguyen"},{"full_name":"Torgrimson, Megan R.","first_name":"Megan R.","last_name":"Torgrimson"},{"last_name":"Parico","first_name":"Gian Carlo G.","full_name":"Parico, Gian Carlo G."},{"first_name":"Sarvind","full_name":"Tripathi, Sarvind","last_name":"Tripathi"},{"last_name":"Zheng","full_name":"Zheng, Ning","first_name":"Ning"},{"last_name":"Lander","first_name":"Gabriel C.","full_name":"Lander, Gabriel C."},{"last_name":"Hirota","full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi"},{"last_name":"Tama","full_name":"Tama, Florence","first_name":"Florence"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"_id":"15147","abstract":[{"text":"Circadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify a key biochemical and structural difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. While both cryptochromes bind the BMAL1 transactivation domain with similar affinity to sequester it from coactivators, CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We identify a dynamic loop in the secondary pocket that regulates differential binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2 forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1 both with and without PER2.","lang":"eng"}],"oa_version":"Preprint","title":"Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/740464","open_access":"1"}],"extern":"1","day":"20","month":"08","status":"public","fulldoi":"https://doi.org/10.1101/740464","doi":"10.1101/740464","article_processing_charge":"No","year":"2019","date_created":"2024-03-21T07:51:10Z","publication_status":"published","date_updated":"2025-09-24T09:00:03Z","publication":"bioRxiv","oa":1,"language":[{"iso":"eng"}],"date_published":"2019-08-20T00:00:00Z"},{"quality_controlled":"1","date_updated":"2024-03-25T12:22:54Z","intvolume":"         6","date_published":"2017-08-01T00:00:00Z","pmid":1,"publication":"eLife","scopus_import":"1","article_processing_charge":"Yes","doi":"10.7554/elife.26163","fulldoi":"https://doi.org/10.7554/elife.26163","article_type":"original","publication_status":"published","date_created":"2024-03-21T07:55:36Z","year":"2017","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","day":"01","month":"08","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Biofilm formation is critical for the infection cycle of Vibrio cholerae. Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are required for the development of biofilm architecture. We demonstrate that RbmA binds VPS directly and uses a binary structural switch within its first fibronectin type III (FnIII-1) domain to control RbmA structural dynamics and the formation of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates interactions in trans with the FnIII-2 domain, leading to open (monomeric) or closed (dimeric) interfaces. The ability of RbmA to switch between open and closed states is important for V. cholerae biofilm formation, as RbmA variants with switches that are locked in either of the two states lead to biofilms with altered architecture and structural integrity."}],"_id":"15154","external_id":{"pmid":["28762945"]},"publisher":"eLife Sciences Publications","oa":1,"language":[{"iso":"eng"}],"volume":6,"publication_identifier":{"issn":["2050-084X"]},"main_file_link":[{"url":"https://doi.org/10.7554/eLife.26163","open_access":"1"}],"article_number":"26163","type":"journal_article","author":[{"last_name":"Fong","first_name":"Jiunn CN","full_name":"Fong, Jiunn CN"},{"first_name":"Andrew","full_name":"Rogers, Andrew","last_name":"Rogers"},{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen"},{"last_name":"Parsley","full_name":"Parsley, Nicole C","first_name":"Nicole C"},{"full_name":"Cornell, William-Cole","first_name":"William-Cole","last_name":"Cornell"},{"first_name":"Yu-Cheng","full_name":"Lin, Yu-Cheng","last_name":"Lin"},{"last_name":"Singh","full_name":"Singh, Praveen K","first_name":"Praveen K"},{"last_name":"Hartmann","first_name":"Raimo","full_name":"Hartmann, Raimo"},{"first_name":"Knut","full_name":"Drescher, Knut","last_name":"Drescher"},{"full_name":"Vinogradov, Evgeny","first_name":"Evgeny","last_name":"Vinogradov"},{"full_name":"Dietrich, Lars EP","first_name":"Lars EP","last_name":"Dietrich"},{"first_name":"Carrie L","full_name":"Partch, Carrie L","last_name":"Partch"},{"full_name":"Yildiz, Fitnat H","first_name":"Fitnat H","last_name":"Yildiz"}],"citation":{"ieee":"J. C. Fong <i>et al.</i>, “Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","ama":"Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.26163\">10.7554/elife.26163</a>","short":"J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.-C. Cornell, Y.-C. Lin, P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch, F.H. Yildiz, ELife 6 (2017).","apa":"Fong, J. C., Rogers, A., Michael, A. K., Parsley, N. C., Cornell, W.-C., Lin, Y.-C., … Yildiz, F. H. (2017). Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.26163\">https://doi.org/10.7554/elife.26163</a>","ista":"Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. 2017. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife. 6, 26163.","mla":"Fong, Jiunn CN, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” <i>ELife</i>, vol. 6, 26163, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.26163\">10.7554/elife.26163</a>.","chicago":"Fong, Jiunn CN, Andrew Rogers, Alicia K. Michael, Nicole C Parsley, William-Cole Cornell, Yu-Cheng Lin, Praveen K Singh, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.26163\">https://doi.org/10.7554/elife.26163</a>."}},{"publisher":"Elsevier","language":[{"iso":"eng"}],"oa":1,"page":"447-457.e7","publication_identifier":{"issn":["1097-2765"]},"volume":66,"issue":"4","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2017.04.011"}],"citation":{"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.","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>","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>","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.","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>.","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>."},"author":[{"first_name":"Chelsea L.","full_name":"Gustafson, Chelsea L.","last_name":"Gustafson"},{"last_name":"Parsley","full_name":"Parsley, Nicole C.","first_name":"Nicole C."},{"full_name":"Asimgil, Hande","first_name":"Hande","last_name":"Asimgil"},{"last_name":"Lee","full_name":"Lee, Hsiau-Wei","first_name":"Hsiau-Wei"},{"last_name":"Ahlbach","first_name":"Christopher","full_name":"Ahlbach, Christopher"},{"last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen"},{"last_name":"Xu","first_name":"Haiyan","full_name":"Xu, Haiyan"},{"full_name":"Williams, Owen L.","first_name":"Owen L.","last_name":"Williams"},{"first_name":"Tara L.","full_name":"Davis, Tara L.","last_name":"Davis"},{"last_name":"Liu","full_name":"Liu, Andrew C.","first_name":"Andrew C."},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"intvolume":"        66","date_updated":"2024-03-25T12:19:20Z","quality_controlled":"1","publication":"Molecular Cell","date_published":"2017-05-18T00:00:00Z","doi":"10.1016/j.molcel.2017.04.011","fulldoi":"https://doi.org/10.1016/j.molcel.2017.04.011","scopus_import":"1","article_processing_charge":"No","year":"2017","article_type":"original","date_created":"2024-03-21T07:56:01Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms","extern":"1","status":"public","month":"05","day":"18","keyword":["Cell Biology","Molecular Biology"],"oa_version":"Published Version","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"}],"_id":"15155"},{"doi":"10.1126/science.aag2516","fulldoi":"https://doi.org/10.1126/science.aag2516","article_processing_charge":"No","scopus_import":"1","year":"2017","publication_status":"published","date_created":"2024-03-21T07:56:24Z","article_type":"original","intvolume":"       355","quality_controlled":"1","date_updated":"2024-03-25T12:16:44Z","publication":"Science","date_published":"2017-03-17T00:00:00Z","oa_version":"None","abstract":[{"text":"Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.","lang":"eng"}],"_id":"15156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structural basis of the day-night transition in a bacterial circadian clock","extern":"1","status":"public","month":"03","day":"17","keyword":["Multidisciplinary"],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"volume":355,"publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"page":"1174-1180","citation":{"short":"R. Tseng, N.F. Goularte, A. Chavan, J. Luu, S.E. Cohen, Y.-G. Chang, J. Heisler, S. Li, A.K. Michael, S. Tripathi, S.S. Golden, A. LiWang, C.L. Partch, Science 355 (2017) 1174–1180.","ieee":"R. Tseng <i>et al.</i>, “Structural basis of the day-night transition in a bacterial circadian clock,” <i>Science</i>, vol. 355, no. 6330. American Association for the Advancement of Science, pp. 1174–1180, 2017.","ama":"Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition in a bacterial circadian clock. <i>Science</i>. 2017;355(6330):1174-1180. doi:<a href=\"https://doi.org/10.1126/science.aag2516\">10.1126/science.aag2516</a>","chicago":"Tseng, Roger, Nicolette F. Goularte, Archana Chavan, Jansen Luu, Susan E. Cohen, Yong-Gang Chang, Joel Heisler, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aag2516\">https://doi.org/10.1126/science.aag2516</a>.","mla":"Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” <i>Science</i>, vol. 355, no. 6330, American Association for the Advancement of Science, 2017, pp. 1174–80, doi:<a href=\"https://doi.org/10.1126/science.aag2516\">10.1126/science.aag2516</a>.","ista":"Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang Y-G, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. 2017. Structural basis of the day-night transition in a bacterial circadian clock. Science. 355(6330), 1174–1180.","apa":"Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G., … Partch, C. L. (2017). Structural basis of the day-night transition in a bacterial circadian clock. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aag2516\">https://doi.org/10.1126/science.aag2516</a>"},"author":[{"first_name":"Roger","full_name":"Tseng, Roger","last_name":"Tseng"},{"full_name":"Goularte, Nicolette F.","first_name":"Nicolette F.","last_name":"Goularte"},{"last_name":"Chavan","first_name":"Archana","full_name":"Chavan, Archana"},{"last_name":"Luu","full_name":"Luu, Jansen","first_name":"Jansen"},{"last_name":"Cohen","full_name":"Cohen, Susan E.","first_name":"Susan E."},{"full_name":"Chang, Yong-Gang","first_name":"Yong-Gang","last_name":"Chang"},{"full_name":"Heisler, Joel","first_name":"Joel","last_name":"Heisler"},{"last_name":"Li","full_name":"Li, Sheng","first_name":"Sheng"},{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen"},{"full_name":"Tripathi, Sarvind","first_name":"Sarvind","last_name":"Tripathi"},{"last_name":"Golden","full_name":"Golden, Susan S.","first_name":"Susan S."},{"full_name":"LiWang, Andy","first_name":"Andy","last_name":"LiWang"},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"issue":"6330","type":"journal_article"},{"author":[{"first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen","last_name":"Michael"},{"last_name":"Fribourgh","full_name":"Fribourgh, Jennifer L.","first_name":"Jennifer L."},{"last_name":"Chelliah","first_name":"Yogarany","full_name":"Chelliah, Yogarany"},{"last_name":"Sandate","first_name":"Colby R.","full_name":"Sandate, Colby R."},{"full_name":"Hura, Greg L.","first_name":"Greg L.","last_name":"Hura"},{"last_name":"Schneidman-Duhovny","full_name":"Schneidman-Duhovny, Dina","first_name":"Dina"},{"full_name":"Tripathi, Sarvind M.","first_name":"Sarvind M.","last_name":"Tripathi"},{"last_name":"Takahashi","first_name":"Joseph S.","full_name":"Takahashi, Joseph S."},{"last_name":"Partch","first_name":"Carrie L.","full_name":"Partch, Carrie L."}],"citation":{"chicago":"Michael, Alicia K., Jennifer L. Fribourgh, Yogarany Chelliah, Colby R. Sandate, Greg L. Hura, Dina Schneidman-Duhovny, Sarvind M. Tripathi, Joseph S. Takahashi, and Carrie L. Partch. “Formation of a Repressive Complex in the Mammalian Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1615310114\">https://doi.org/10.1073/pnas.1615310114</a>.","apa":"Michael, A. K., Fribourgh, J. L., Chelliah, Y., Sandate, C. R., Hura, G. L., Schneidman-Duhovny, D., … Partch, C. L. (2017). Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1615310114\">https://doi.org/10.1073/pnas.1615310114</a>","ista":"Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny D, Tripathi SM, Takahashi JS, Partch CL. 2017. Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proceedings of the National Academy of Sciences. 114(7), 1560–1565.","mla":"Michael, Alicia K., et al. “Formation of a Repressive Complex in the Mammalian Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 7, Proceedings of the National Academy of Sciences, 2017, pp. 1560–65, doi:<a href=\"https://doi.org/10.1073/pnas.1615310114\">10.1073/pnas.1615310114</a>.","short":"A.K. Michael, J.L. Fribourgh, Y. Chelliah, C.R. Sandate, G.L. Hura, D. Schneidman-Duhovny, S.M. Tripathi, J.S. Takahashi, C.L. Partch, Proceedings of the National Academy of Sciences 114 (2017) 1560–1565.","ieee":"A. K. Michael <i>et al.</i>, “Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 7. Proceedings of the National Academy of Sciences, pp. 1560–1565, 2017.","ama":"Michael AK, Fribourgh JL, Chelliah Y, et al. Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(7):1560-1565. doi:<a href=\"https://doi.org/10.1073/pnas.1615310114\">10.1073/pnas.1615310114</a>"},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1615310114","open_access":"1"}],"issue":"7","type":"journal_article","volume":114,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"page":"1560-1565","language":[{"iso":"eng"}],"oa":1,"publisher":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["28143926"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The basic helix–loop–helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1."}],"_id":"15157","keyword":["Multidisciplinary"],"status":"public","day":"31","month":"01","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1","article_type":"original","publication_status":"published","date_created":"2024-03-21T07:56:50Z","year":"2017","scopus_import":"1","article_processing_charge":"No","doi":"10.1073/pnas.1615310114","fulldoi":"https://doi.org/10.1073/pnas.1615310114","date_published":"2017-01-31T00:00:00Z","pmid":1,"publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","date_updated":"2024-03-25T12:12:23Z","intvolume":"       114"},{"publication_identifier":{"issn":["0031-8655"],"eissn":["1751-1097"]},"volume":93,"oa":1,"language":[{"iso":"eng"}],"page":"128-140","publisher":"Wiley","citation":{"short":"A.K. Michael, J.L. Fribourgh, R.N. Van Gelder, C.L. Partch, Photochemistry and Photobiology 93 (2017) 128–140.","ama":"Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. <i>Photochemistry and Photobiology</i>. 2017;93(1):128-140. doi:<a href=\"https://doi.org/10.1111/php.12677\">10.1111/php.12677</a>","ieee":"A. K. Michael, J. L. Fribourgh, R. N. Van Gelder, and C. L. Partch, “Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond,” <i>Photochemistry and Photobiology</i>, vol. 93, no. 1. Wiley, pp. 128–140, 2017.","chicago":"Michael, Alicia K., Jennifer L. Fribourgh, Russell N. Van Gelder, and Carrie L. Partch. “Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond.” <i>Photochemistry and Photobiology</i>. Wiley, 2017. <a href=\"https://doi.org/10.1111/php.12677\">https://doi.org/10.1111/php.12677</a>.","ista":"Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. 2017. Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. 93(1), 128–140.","mla":"Michael, Alicia K., et al. “Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond.” <i>Photochemistry and Photobiology</i>, vol. 93, no. 1, Wiley, 2017, pp. 128–40, doi:<a href=\"https://doi.org/10.1111/php.12677\">10.1111/php.12677</a>.","apa":"Michael, A. K., Fribourgh, J. L., Van Gelder, R. N., &#38; Partch, C. L. (2017). Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. <i>Photochemistry and Photobiology</i>. Wiley. <a href=\"https://doi.org/10.1111/php.12677\">https://doi.org/10.1111/php.12677</a>"},"author":[{"first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen","last_name":"Michael"},{"last_name":"Fribourgh","first_name":"Jennifer L.","full_name":"Fribourgh, Jennifer L."},{"full_name":"Van Gelder, Russell N.","first_name":"Russell N.","last_name":"Van Gelder"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"type":"journal_article","issue":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/php.12677"}],"year":"2017","publication_status":"published","date_created":"2024-03-21T07:57:18Z","article_type":"original","doi":"10.1111/php.12677","fulldoi":"https://doi.org/10.1111/php.12677","article_processing_charge":"No","scopus_import":"1","publication":"Photochemistry and Photobiology","date_published":"2017-02-01T00:00:00Z","intvolume":"        93","quality_controlled":"1","date_updated":"2024-03-25T12:09:21Z","oa_version":"Published Version","_id":"15158","abstract":[{"text":"Cryptochromes are evolutionarily related to the light‐dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: <jats:italic>Drosophila</jats:italic>‐like CRYs that act as nonvisual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate‐like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors. Some animals have both types of CRYs, while others possess only one. Cryptochromes have two domains, the photolyase homology region (PHR) and an extended, intrinsically disordered C‐terminus. While all animal CRYs share a high degree of sequence and structural homology in their PHR domains, the C‐termini are divergent in both length and sequence identity. Recently, cryptochrome function has been shown to extend beyond its pivotal role in circadian clocks, participating in regulation of the DNA damage response, cancer progression and glucocorticoid signaling, as well as being implicated as possible magnetoreceptors. In this review, we provide a historical perspective on the discovery of animal cryptochromes, examine similarities and differences of the two types of animal cryptochromes and explore some of the divergent roles for this class of proteins.","lang":"eng"}],"status":"public","day":"01","month":"02","keyword":["Physical and Theoretical Chemistry","General Medicine","Biochemistry"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond","extern":"1"},{"type":"journal_article","issue":"9","author":[{"last_name":"Michael","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen"},{"last_name":"Asimgil","full_name":"Asimgil, Hande","first_name":"Hande"},{"last_name":"Partch","first_name":"Carrie L.","full_name":"Partch, Carrie L."}],"citation":{"apa":"Michael, A. K., Asimgil, H., &#38; Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. <i>Trends in Biochemical Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">https://doi.org/10.1016/j.tibs.2015.07.006</a>","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” <i>Trends in Biochemical Sciences</i>, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:<a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">10.1016/j.tibs.2015.07.006</a>.","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” <i>Trends in Biochemical Sciences</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">https://doi.org/10.1016/j.tibs.2015.07.006</a>.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. <i>Trends in Biochemical Sciences</i>. 2015;40(9):489-490. doi:<a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">10.1016/j.tibs.2015.07.006</a>","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” <i>Trends in Biochemical Sciences</i>, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490."},"page":"489-490","language":[{"iso":"eng"}],"publisher":"Elsevier","volume":40,"publication_identifier":{"issn":["0968-0004"]},"keyword":["Molecular Biology","Biochemistry"],"status":"public","month":"09","day":"01","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cytosolic BMAL1 moonlights as a translation factor","oa_version":"None","abstract":[{"text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling.","lang":"eng"}],"_id":"15159","date_published":"2015-09-01T00:00:00Z","publication":"Trends in Biochemical Sciences","date_updated":"2024-03-25T11:53:58Z","quality_controlled":"1","intvolume":"        40","publication_status":"published","date_created":"2024-03-21T07:57:44Z","article_type":"original","year":"2015","article_processing_charge":"No","scopus_import":"1","doi":"10.1016/j.tibs.2015.07.006","fulldoi":"https://doi.org/10.1016/j.tibs.2015.07.006"},{"page":"743-754","oa":1,"language":[{"iso":"eng"}],"publisher":"Elsevier","volume":58,"publication_identifier":{"issn":["1097-2765"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2015.03.031","open_access":"1"}],"type":"journal_article","issue":"5","author":[{"last_name":"Michael","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"last_name":"Harvey","first_name":"Stacy L.","full_name":"Harvey, Stacy L."},{"full_name":"Sammons, Patrick J.","first_name":"Patrick J.","last_name":"Sammons"},{"first_name":"Amanda P.","full_name":"Anderson, Amanda P.","last_name":"Anderson"},{"full_name":"Kopalle, Hema M.","first_name":"Hema M.","last_name":"Kopalle"},{"last_name":"Banham","full_name":"Banham, Alison H.","first_name":"Alison H."},{"last_name":"Partch","first_name":"Carrie L.","full_name":"Partch, Carrie L."}],"citation":{"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>","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.","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.","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>","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>.","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>."},"date_published":"2015-06-04T00:00:00Z","publication":"Molecular Cell","date_updated":"2024-03-25T11:52:26Z","quality_controlled":"1","intvolume":"        58","publication_status":"published","date_created":"2024-03-21T07:58:08Z","article_type":"original","year":"2015","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.molcel.2015.03.031","doi":"10.1016/j.molcel.2015.03.031","keyword":["Cell Biology","Molecular Biology"],"month":"06","day":"04","status":"public","extern":"1","title":"Cancer/Testis antigen PASD1 silences the circadian clock","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15160","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"}],"oa_version":"Published Version"},{"publication_identifier":{"eissn":["1520-6904"],"issn":["0022-3263"]},"volume":79,"oa":1,"language":[{"iso":"eng"}],"page":"7199-7204","publisher":"American Chemical Society","citation":{"chicago":"Guan, Weiye, Alicia K. Michael, Melissa L. McIntosh, Liza Koren-Selfridge, John P. Scott, and Timothy B. Clark. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” <i>The Journal of Organic Chemistry</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/jo500773t\">https://doi.org/10.1021/jo500773t</a>.","mla":"Guan, Weiye, et al. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” <i>The Journal of Organic Chemistry</i>, vol. 79, no. 15, American Chemical Society, 2014, pp. 7199–204, doi:<a href=\"https://doi.org/10.1021/jo500773t\">10.1021/jo500773t</a>.","ista":"Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. 2014. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 79(15), 7199–7204.","apa":"Guan, W., Michael, A. K., McIntosh, M. L., Koren-Selfridge, L., Scott, J. P., &#38; Clark, T. B. (2014). Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. <i>The Journal of Organic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jo500773t\">https://doi.org/10.1021/jo500773t</a>","short":"W. Guan, A.K. Michael, M.L. McIntosh, L. Koren-Selfridge, J.P. Scott, T.B. Clark, The Journal of Organic Chemistry 79 (2014) 7199–7204.","ieee":"W. Guan, A. K. Michael, M. L. McIntosh, L. Koren-Selfridge, J. P. Scott, and T. B. Clark, “Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters,” <i>The Journal of Organic Chemistry</i>, vol. 79, no. 15. American Chemical Society, pp. 7199–7204, 2014.","ama":"Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. <i>The Journal of Organic Chemistry</i>. 2014;79(15):7199-7204. doi:<a href=\"https://doi.org/10.1021/jo500773t\">10.1021/jo500773t</a>"},"author":[{"last_name":"Guan","first_name":"Weiye","full_name":"Guan, Weiye"},{"first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen","last_name":"Michael"},{"last_name":"McIntosh","first_name":"Melissa L.","full_name":"McIntosh, Melissa L."},{"last_name":"Koren-Selfridge","first_name":"Liza","full_name":"Koren-Selfridge, Liza"},{"first_name":"John P.","full_name":"Scott, John P.","last_name":"Scott"},{"last_name":"Clark","full_name":"Clark, Timothy B.","first_name":"Timothy B."}],"issue":"15","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1021/jo500773t","open_access":"1"}],"year":"2014","article_type":"letter_note","date_created":"2024-03-21T07:58:31Z","publication_status":"published","doi":"10.1021/jo500773t","fulldoi":"https://doi.org/10.1021/jo500773t","scopus_import":"1","article_processing_charge":"No","publication":"The Journal of Organic Chemistry","date_published":"2014-06-10T00:00:00Z","intvolume":"        79","quality_controlled":"1","date_updated":"2024-03-25T11:50:01Z","oa_version":"Published Version","_id":"15161","abstract":[{"lang":"eng","text":"The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate esters with moderate to good yields and selectivity. Addition of tosic acid to the crude diboration products provides the corresponding vinyl boronate esters upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling reaction to obtain alkenes of known geometry."}],"status":"public","day":"10","month":"06","keyword":["Organic Chemistry"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters","extern":"1"}]