--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21509' abstract: - lang: eng text: Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes. 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). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Luca full_name: Vecchia, Luca last_name: Vecchia - first_name: David full_name: Domjan, David last_name: Domjan - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Anton full_name: Sabantsev, Anton last_name: Sabantsev - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Ganesh R. full_name: Pathare, Ganesh R. last_name: Pathare - first_name: Klaus full_name: Brackmann, Klaus last_name: Brackmann - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Lukas full_name: Kater, Lukas last_name: Kater - first_name: Eric full_name: Hietter-Pfeiffer, Eric last_name: Hietter-Pfeiffer - first_name: Mina full_name: Haddawi, Mina last_name: Haddawi - first_name: Urja P. full_name: Kuber, Urja P. last_name: Kuber - first_name: Sandra full_name: Mühlhäusser, Sandra last_name: Mühlhäusser - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Michael B. full_name: Stadler, Michael B. last_name: Stadler - first_name: Sebastian full_name: Deindl, Sebastian last_name: Deindl - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 2026;86(4):625-639.e8. doi:10.1016/j.molcel.2026.01.021 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. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2026.01.021 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.” Molecular Cell. Elsevier, 2026. https://doi.org/10.1016/j.molcel.2026.01.021. ieee: J. Weiss et al., “The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2,” Molecular Cell, vol. 86, no. 4. Elsevier, p. 625–639.e8, 2026. ista: Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 86(4), 625–639.e8. mla: Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell, vol. 86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:10.1016/j.molcel.2026.01.021. 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. date_created: 2026-03-30T11:58:48Z date_published: 2026-02-19T00:00:00Z date_updated: 2026-03-30T12:09:08Z day: '19' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.molcel.2026.01.021 external_id: pmid: - '41679301' file: - access_level: open_access checksum: e16a7315b64a706184b177ea1621523c content_type: application/pdf creator: dernst date_created: 2026-03-30T12:04:38Z date_updated: 2026-03-30T12:04:38Z file_id: '21510' file_name: 2026_MolecularCell_Weiss.pdf file_size: 9786677 relation: main_file success: 1 file_date_updated: 2026-03-30T12:04:38Z fulldoi: https://doi.org/10.1016/j.molcel.2026.01.021 has_accepted_license: '1' intvolume: ' 86' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 625-639.e8 pmid: 1 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20924' abstract: - lang: eng text: "Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1" acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.). article_number: '104295' article_processing_charge: Yes article_type: original author: - first_name: Wataru full_name: Kobayashi, Wataru last_name: Kobayashi - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Siwat full_name: Ruangroengkulrith, Siwat last_name: Ruangroengkulrith - first_name: Maximilian full_name: Kümmecke, Maximilian last_name: Kümmecke - first_name: Kikuë full_name: Tachibana, Kikuë last_name: Tachibana citation: 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. STAR Protocols. 2026;7(1). doi:10.1016/j.xpro.2025.104295 apa: Kobayashi, W., Michael, A. K., 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. Elsevier. https://doi.org/10.1016/j.xpro.2025.104295 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.” STAR Protocols. Elsevier, 2026. https://doi.org/10.1016/j.xpro.2025.104295. 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,” STAR Protocols, vol. 7, no. 1. Elsevier, 2026. 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. mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” STAR Protocols, vol. 7, no. 1, 104295, Elsevier, 2026, doi:10.1016/j.xpro.2025.104295. short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2026). corr_author: '1' das_tickbox: '1' 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. date_created: 2026-01-04T23:01:33Z date_published: 2026-03-20T00:00:00Z date_updated: 2026-07-23T06:34:37Z day: '20' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.xpro.2025.104295 external_id: pmid: - '41455105' file: - access_level: open_access checksum: cf04b061a48548a649e6a2435bf120db content_type: application/pdf creator: dernst date_created: 2026-07-23T06:33:24Z date_updated: 2026-07-23T06:33:24Z file_id: '22389' file_name: 2026_StarProtocols_Kobayashi.pdf file_size: 5531906 relation: main_file success: 1 file_date_updated: 2026-07-23T06:33:24Z fulldoi: https://doi.org/10.1016/j.xpro.2025.104295 has_accepted_license: '1' intvolume: ' 7' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9136c684-16d5-11f0-9cad-91c0177b365f grant_number: '101162145' name: Circadian structural transitions of chromatin publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20935' abstract: - lang: eng text: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics. acknowledgement: Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ron full_name: Kelley, Ron last_name: Kelley - first_name: Sagar full_name: Khavnekar, Sagar last_name: Khavnekar - first_name: Ricardo D. full_name: Righetto, Ricardo D. last_name: Righetto - first_name: Jessica full_name: Heebner, Jessica last_name: Heebner - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Xianjun full_name: Zhang, Xianjun last_name: Zhang - first_name: Saikat full_name: Chakraborty, Saikat last_name: Chakraborty - first_name: Grigory full_name: Tagiltsev, Grigory last_name: Tagiltsev - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Sofie full_name: Van Dorst, Sofie last_name: Van Dorst - first_name: Florent full_name: Waltz, Florent last_name: Waltz - first_name: Caitlyn L. full_name: Mccafferty, Caitlyn L. last_name: Mccafferty - first_name: Lorenz full_name: Lamm, Lorenz last_name: Lamm - first_name: Simon full_name: Zufferey, Simon last_name: Zufferey - first_name: Philippe full_name: Van Der Stappen, Philippe last_name: Van Der Stappen - first_name: Hugo full_name: Van Den Hoek, Hugo last_name: Van Den Hoek - first_name: Wojciech full_name: Wietrzynski, Wojciech last_name: Wietrzynski - first_name: Pavol full_name: Harar, Pavol id: e03d953a-6e8c-11ef-99e4-f0717d385cd5 last_name: Harar orcid: 0000-0001-5206-1794 - first_name: William full_name: Wan, William last_name: Wan - first_name: John A.G. full_name: Briggs, John A.G. last_name: Briggs - first_name: Jürgen M. full_name: Plitzko, Jürgen M. last_name: Plitzko - first_name: Benjamin D. full_name: Engel, Benjamin D. last_name: Engel - first_name: Abhay full_name: Kotecha, Abhay last_name: Kotecha citation: ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 2026;86(1):213-230.e7. doi:10.1016/j.molcel.2025.11.029 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. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029 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.” Molecular Cell. Elsevier, 2026. https://doi.org/10.1016/j.molcel.2025.11.029. ieee: R. Kelley et al., “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell, vol. 86, no. 1. Elsevier, p. 213–230.e7, 2026. 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.” Molecular Cell, vol. 86, no. 1, Elsevier, 2026, p. 213–230.e7, doi:10.1016/j.molcel.2025.11.029. 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. das_tickbox: '1' 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." date_created: 2026-01-04T23:01:36Z date_published: 2026-01-08T00:00:00Z date_updated: 2026-07-28T07:39:23Z day: '08' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.molcel.2025.11.029 file: - access_level: open_access checksum: 96a2f8519124d1a0d9de8d2594bf7147 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:38:45Z date_updated: 2026-07-28T07:38:45Z file_id: '22599' file_name: 2026_MolecularCell_Kelley.pdf file_size: 26749637 relation: main_file success: 1 file_date_updated: 2026-07-28T07:38:45Z fulldoi: https://doi.org/10.1016/j.molcel.2025.11.029 has_accepted_license: '1' intvolume: ' 86' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 213-230.e7 publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22720' abstract: - lang: eng 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. 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Fatih full_name: Aygenli, Fatih last_name: Aygenli - first_name: Lukas A. full_name: Huschet, Lukas A. last_name: Huschet - first_name: Tanja full_name: Popp, Tanja last_name: Popp - first_name: Andrea full_name: Ribeiro, Andrea last_name: Ribeiro - first_name: Darina full_name: Barkhatova, Darina id: db547c8c-329f-11ee-a353-cde802618f9e last_name: Barkhatova orcid: 0000-0002-0062-2817 - first_name: Céline full_name: Jouffe, Céline last_name: Jouffe - first_name: Ricardo full_name: Trozzo, Ricardo last_name: Trozzo - first_name: Jerome S. full_name: Menet, Jerome S. last_name: Menet - first_name: Roland full_name: Rad, Roland last_name: Rad - first_name: Kenneth A. full_name: Dyar, Kenneth A. last_name: Dyar - first_name: Maciej full_name: Lech, Maciej last_name: Lech - first_name: Tobias full_name: Straub, Tobias last_name: Straub - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Maria S. full_name: Robles, Maria S. last_name: Robles citation: ama: Aygenli F, Huschet LA, Popp T, et al. CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators. Nature Cell Biology. 2026. doi:10.1038/s41556-026-02041-4 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. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-026-02041-4 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.” Nature Cell Biology. Springer Nature, 2026. https://doi.org/10.1038/s41556-026-02041-4. ieee: F. Aygenli et al., “CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators,” Nature Cell Biology. Springer Nature, 2026. 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.” Nature Cell Biology, Springer Nature, 2026, doi:10.1038/s41556-026-02041-4. 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). das_tickbox: '1' 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. date_created: 2026-08-16T22:01:44Z date_published: 2026-08-06T00:00:00Z date_updated: 2026-08-18T08:03:22Z day: '06' ddc: - '570' department: - _id: GradSch - _id: AlMi doi: 10.1038/s41556-026-02041-4 external_id: pmid: - '42562924' fulldoi: https://doi.org/10.1038/s41556-026-02041-4 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41556-026-02041-4 month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9136c684-16d5-11f0-9cad-91c0177b365f grant_number: '101162145' name: Circadian structural transitions of chromatin publication: Nature Cell Biology publication_identifier: eissn: - 1476-4679 issn: - 1465-7392 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _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. 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.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Deyasini full_name: Chakraborty, Deyasini last_name: Chakraborty - first_name: Colby R. full_name: Sandate, Colby R. last_name: Sandate - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Lukas full_name: Kater, Lukas last_name: Kater - first_name: Jan full_name: Seebacher, Jan last_name: Seebacher - first_name: Zuzanna full_name: Kozicka, Zuzanna last_name: Kozicka - first_name: Lisa full_name: Stoos, Lisa last_name: Stoos - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access to p53. Molecular Cell. 2025;85(15):2919-2936.e12. doi:10.1016/j.molcel.2025.06.027 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. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.06.027 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.” Molecular Cell. Elsevier, 2025. https://doi.org/10.1016/j.molcel.2025.06.027. ieee: D. Chakraborty et al., “Nucleosomes specify co-factor access to p53,” Molecular Cell, vol. 85, no. 15. Elsevier, p. 2919–2936.e12, 2025. 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. mla: Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.” Molecular Cell, vol. 85, no. 15, Elsevier, 2025, p. 2919–2936.e12, doi:10.1016/j.molcel.2025.06.027. 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. date_created: 2025-09-23T08:56:13Z date_published: 2025-08-07T00:00:00Z date_updated: 2025-09-24T08:21:55Z day: '07' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.molcel.2025.06.027 file: - access_level: open_access checksum: e60390ca629b350af3221d4718ca6534 content_type: application/pdf creator: dernst date_created: 2025-09-24T07:54:03Z date_updated: 2025-09-24T07:54:03Z file_id: '20386' file_name: 2025_MolecularCell_Chakraborty.pdf file_size: 41813494 relation: main_file success: 1 file_date_updated: 2025-09-24T07:54:03Z fulldoi: https://doi.org/10.1016/j.molcel.2025.06.027 has_accepted_license: '1' intvolume: ' 85' issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 2919-2936.e12 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nucleosomes specify co-factor access to p53 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2025' ... --- _id: '15148' 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 members1. 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. 2,3). 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 patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5–7 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.' article_processing_charge: No article_type: original author: - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - 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 - first_name: Kristina full_name: Makasheva, Kristina last_name: Makasheva - first_name: Martina full_name: Minnich, Martina last_name: Minnich - first_name: Kelly L. full_name: Healy, Kelly L. last_name: Healy - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Lukas full_name: Kater, Lukas last_name: Kater - first_name: Jan full_name: Seebacher, Jan last_name: Seebacher - first_name: Luca full_name: Vecchia, Luca last_name: Vecchia - first_name: Deyasini full_name: Chakraborty, Deyasini last_name: Chakraborty - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Florian full_name: Andersch, Florian last_name: Andersch - first_name: Jennifer L. full_name: Fribourgh, Jennifer L. last_name: Fribourgh - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler - first_name: Johannes full_name: Zuber, Johannes last_name: Zuber - first_name: Andrew C. full_name: Liu, Andrew C. last_name: Liu - first_name: Peter B. full_name: Becker, Peter B. last_name: Becker - first_name: Beat full_name: Fierz, Beat last_name: Fierz - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch - first_name: Jerome S. full_name: Menet, Jerome S. last_name: Menet - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Michael AK, Stoos L, Crosby P, et al. Cooperation between bHLH transcription factors and histones for DNA access. Nature. 2023;619(7969):385-393. doi:10.1038/s41586-023-06282-3 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. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06282-3 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.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06282-3. ieee: A. K. Michael et al., “Cooperation between bHLH transcription factors and histones for DNA access,” Nature, vol. 619, no. 7969. Springer Nature, pp. 385–393, 2023. 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.” Nature, vol. 619, no. 7969, Springer Nature, 2023, pp. 385–93, doi:10.1038/s41586-023-06282-3. 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. date_created: 2024-03-21T07:52:44Z date_published: 2023-07-05T00:00:00Z date_updated: 2024-03-25T12:42:29Z day: '05' doi: 10.1038/s41586-023-06282-3 extern: '1' fulldoi: https://doi.org/10.1038/s41586-023-06282-3 intvolume: ' 619' issue: '7969' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41586-023-06282-3 month: '07' oa: 1 oa_version: Published Version page: 385-393 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cooperation between bHLH transcription factors and histones for DNA access type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 619 year: '2023' ... --- _id: '15149' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Murat full_name: Iskar, Murat last_name: Iskar - first_name: Sevi full_name: Durdu, Sevi last_name: Durdu - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Eric full_name: Hietter-Pfeiffer, Eric last_name: Hietter-Pfeiffer - first_name: Zuzanna full_name: Kozicka, Zuzanna last_name: Kozicka - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Lukas full_name: Burger, Lukas last_name: Burger - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler citation: ama: Isbel L, Iskar M, Durdu S, et al. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural & Molecular Biology. 2023;30(7):948-957. doi:10.1038/s41594-023-01021-8 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. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01021-8 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.” Nature Structural & Molecular Biology. Springer Nature, 2023. https://doi.org/10.1038/s41594-023-01021-8. ieee: L. Isbel et al., “Readout of histone methylation by Trim24 locally restricts chromatin opening by p53,” Nature Structural & Molecular Biology, vol. 30, no. 7. Springer Nature, pp. 948–957, 2023. 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 & Molecular Biology. 30(7), 948–957. mla: Isbel, Luke, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” Nature Structural & Molecular Biology, vol. 30, no. 7, Springer Nature, 2023, pp. 948–57, doi:10.1038/s41594-023-01021-8. 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 & Molecular Biology 30 (2023) 948–957. date_created: 2024-03-21T07:53:24Z date_published: 2023-06-29T00:00:00Z date_updated: 2024-03-25T12:37:20Z day: '29' doi: 10.1038/s41594-023-01021-8 extern: '1' external_id: pmid: - '37386214' fulldoi: https://doi.org/10.1038/s41594-023-01021-8 intvolume: ' 30' issue: '7' keyword: - Molecular Biology - Structural Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41594-023-01021-8 month: '06' oa: 1 oa_version: Published Version page: 948-957 pmid: 1 publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Readout of histone methylation by Trim24 locally restricts chromatin opening by p53 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2023' ... --- _id: '15150' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Lukas full_name: Burger, Lukas last_name: Burger - first_name: Cathrin full_name: Gräwe, Cathrin last_name: Gräwe - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Daniel full_name: Hess, Daniel last_name: Hess - first_name: Leslie full_name: Hoerner, Leslie last_name: Hoerner - first_name: Vytautas full_name: Iesmantavicius, Vytautas last_name: Iesmantavicius - first_name: Sevi full_name: Durdu, Sevi last_name: Durdu - first_name: Marco full_name: Pregnolato, Marco last_name: Pregnolato - first_name: Arnaud R. full_name: Krebs, Arnaud R. last_name: Krebs - first_name: Sébastien A. full_name: Smallwood, Sébastien A. last_name: Smallwood - first_name: Nicolas full_name: Thomä, Nicolas last_name: Thomä - first_name: Michiel full_name: Vermeulen, Michiel last_name: Vermeulen - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler citation: ama: Grand RS, Burger L, Gräwe C, et al. BANP opens chromatin and activates CpG-island-regulated genes. Nature. 2021;596:133-137. doi:10.1038/s41586-021-03689-8 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. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03689-8 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.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03689-8. ieee: R. S. Grand et al., “BANP opens chromatin and activates CpG-island-regulated genes,” Nature, vol. 596. Springer Nature, pp. 133–137, 2021. 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. mla: Grand, Ralph S., et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” Nature, vol. 596, Springer Nature, 2021, pp. 133–37, doi:10.1038/s41586-021-03689-8. 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. date_created: 2024-03-21T07:53:48Z date_published: 2021-08-05T00:00:00Z date_updated: 2024-03-25T12:34:31Z day: '05' doi: 10.1038/s41586-021-03689-8 extern: '1' fulldoi: https://doi.org/10.1038/s41586-021-03689-8 intvolume: ' 596' language: - iso: eng month: '08' oa_version: None page: 133-137 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: BANP opens chromatin and activates CpG-island-regulated genes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 596 year: '2021' ... --- _id: '15151' abstract: - lang: eng 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. article_processing_charge: No article_type: review author: - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611. doi:10.1016/j.cell.2021.05.029 apa: Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029 chicago: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029. ieee: A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021. ista: Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611. mla: Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029. short: A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611. date_created: 2024-03-21T07:54:19Z date_published: 2021-07-08T00:00:00Z date_updated: 2024-03-25T12:31:39Z day: '08' doi: 10.1016/j.cell.2021.05.029 extern: '1' fulldoi: https://doi.org/10.1016/j.cell.2021.05.029 intvolume: ' 184' issue: '14' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2021.05.029 month: '07' oa: 1 oa_version: Published Version page: 3599-3611 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Reading the chromatinized genome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 184 year: '2021' ... --- _id: '15152' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Luke full_name: Isbel, Luke last_name: Isbel - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Zuzanna full_name: Kozicka, Zuzanna last_name: Kozicka - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Richard D. full_name: Bunker, Richard D. last_name: Bunker - first_name: Andreas D. full_name: Schenk, Andreas D. last_name: Schenk - first_name: Alexandra full_name: Graff-Meyer, Alexandra last_name: Graff-Meyer - first_name: Ganesh R. full_name: Pathare, Ganesh R. last_name: Pathare - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Syota full_name: Matsumoto, Syota last_name: Matsumoto - first_name: Lukas full_name: Burger, Lukas last_name: Burger - first_name: Dirk full_name: Schübeler, Dirk last_name: Schübeler - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Michael AK, Grand RS, Isbel L, et al. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science. 2020;368(6498):1460-1465. doi:10.1126/science.abb0074 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. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.abb0074 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.” Science. American Association for the Advancement of Science , 2020. https://doi.org/10.1126/science.abb0074. ieee: A. K. Michael et al., “Mechanisms of OCT4-SOX2 motif readout on nucleosomes,” Science, vol. 368, no. 6498. American Association for the Advancement of Science , pp. 1460–1465, 2020. 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.” Science, vol. 368, no. 6498, American Association for the Advancement of Science , 2020, pp. 1460–65, doi:10.1126/science.abb0074. 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. date_created: 2024-03-21T07:54:44Z date_published: 2020-04-23T00:00:00Z date_updated: 2024-03-25T12:29:34Z day: '23' doi: 10.1126/science.abb0074 extern: '1' fulldoi: https://doi.org/10.1126/science.abb0074 intvolume: ' 368' issue: '6498' language: - iso: eng month: '04' oa_version: None page: 1460-1465 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms of OCT4-SOX2 motif readout on nucleosomes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 368 year: '2020' ... --- _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. article_number: '55275' article_processing_charge: No article_type: original author: - first_name: Jennifer L full_name: Fribourgh, Jennifer L last_name: Fribourgh - first_name: Ashutosh full_name: Srivastava, Ashutosh last_name: Srivastava - first_name: Colby R full_name: Sandate, Colby R last_name: Sandate - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Peter L full_name: Hsu, Peter L last_name: Hsu - first_name: Christin full_name: Rakers, Christin last_name: Rakers - first_name: Leslee T full_name: Nguyen, Leslee T last_name: Nguyen - first_name: Megan R full_name: Torgrimson, Megan R last_name: Torgrimson - first_name: Gian Carlo G full_name: Parico, Gian Carlo G last_name: Parico - first_name: Sarvind full_name: Tripathi, Sarvind last_name: Tripathi - first_name: Ning full_name: Zheng, Ning last_name: Zheng - first_name: Gabriel C full_name: Lander, Gabriel C last_name: Lander - first_name: Tsuyoshi full_name: Hirota, Tsuyoshi last_name: Hirota - first_name: Florence full_name: Tama, Florence last_name: Tama - first_name: Carrie L full_name: Partch, Carrie L last_name: Partch citation: 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. eLife. 2020;9. doi:10.7554/elife.55275 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. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55275 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.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275. ieee: J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife, vol. 9. eLife Sciences Publications, 2020. 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. mla: Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife, vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275. 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). date_created: 2024-03-21T07:55:12Z date_published: 2020-02-26T00:00:00Z date_updated: 2024-03-25T12:25:02Z day: '26' doi: 10.7554/elife.55275 extern: '1' fulldoi: https://doi.org/10.7554/elife.55275 intvolume: ' 9' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/eLife.55275 month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2020' ... --- _id: '15147' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Jennifer L. full_name: Fribourgh, Jennifer L. last_name: Fribourgh - first_name: Ashutosh full_name: Srivastava, Ashutosh last_name: Srivastava - first_name: Colby R. full_name: Sandate, Colby R. last_name: Sandate - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Peter L. full_name: Hsu, Peter L. last_name: Hsu - first_name: Christin full_name: Rakers, Christin last_name: Rakers - first_name: Leslee T. full_name: Nguyen, Leslee T. last_name: Nguyen - first_name: Megan R. full_name: Torgrimson, Megan R. last_name: Torgrimson - first_name: Gian Carlo G. full_name: Parico, Gian Carlo G. last_name: Parico - first_name: Sarvind full_name: Tripathi, Sarvind last_name: Tripathi - first_name: Ning full_name: Zheng, Ning last_name: Zheng - first_name: Gabriel C. full_name: Lander, Gabriel C. last_name: Lander - first_name: Tsuyoshi full_name: Hirota, Tsuyoshi last_name: Hirota - first_name: Florence full_name: Tama, Florence last_name: Tama - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Fribourgh JL, Srivastava A, Sandate CR, et al. Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms. bioRxiv. 2019. doi:10.1101/740464 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. bioRxiv. https://doi.org/10.1101/740464 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.” BioRxiv, 2019. https://doi.org/10.1101/740464. ieee: J. L. Fribourgh et al., “Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms,” bioRxiv. 2019. 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, 10.1101/740464. mla: Fribourgh, Jennifer L., et al. “Protein Dynamics Regulate Distinct Biochemical Properties of Cryptochromes in Mammalian Circadian Rhythms.” BioRxiv, 2019, doi:10.1101/740464. 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). date_created: 2024-03-21T07:51:10Z date_published: 2019-08-20T00:00:00Z date_updated: 2025-09-24T09:00:03Z day: '20' doi: 10.1101/740464 extern: '1' fulldoi: https://doi.org/10.1101/740464 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/740464 month: '08' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published status: public title: Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '15154' 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. article_number: '26163' article_processing_charge: Yes article_type: original author: - first_name: Jiunn CN full_name: Fong, Jiunn CN last_name: Fong - first_name: Andrew full_name: Rogers, Andrew last_name: Rogers - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Nicole C full_name: Parsley, Nicole C last_name: Parsley - first_name: William-Cole full_name: Cornell, William-Cole last_name: Cornell - first_name: Yu-Cheng full_name: Lin, Yu-Cheng last_name: Lin - first_name: Praveen K full_name: Singh, Praveen K last_name: Singh - first_name: Raimo full_name: Hartmann, Raimo last_name: Hartmann - first_name: Knut full_name: Drescher, Knut last_name: Drescher - first_name: Evgeny full_name: Vinogradov, Evgeny last_name: Vinogradov - first_name: Lars EP full_name: Dietrich, Lars EP last_name: Dietrich - first_name: Carrie L full_name: Partch, Carrie L last_name: Partch - first_name: Fitnat H full_name: Yildiz, Fitnat H last_name: Yildiz citation: ama: Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife. 2017;6. doi:10.7554/elife.26163 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. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.26163 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.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.26163. ieee: J. C. Fong et al., “Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms,” eLife, vol. 6. eLife Sciences Publications, 2017. 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.” ELife, vol. 6, 26163, eLife Sciences Publications, 2017, doi:10.7554/elife.26163. 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). date_created: 2024-03-21T07:55:36Z date_published: 2017-08-01T00:00:00Z date_updated: 2024-03-25T12:22:54Z day: '01' doi: 10.7554/elife.26163 extern: '1' external_id: pmid: - '28762945' fulldoi: https://doi.org/10.7554/elife.26163 intvolume: ' 6' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/eLife.26163 month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '15155' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Chelsea L. full_name: Gustafson, Chelsea L. last_name: Gustafson - first_name: Nicole C. full_name: Parsley, Nicole C. last_name: Parsley - first_name: Hande full_name: Asimgil, Hande last_name: Asimgil - first_name: Hsiau-Wei full_name: Lee, Hsiau-Wei last_name: Lee - first_name: Christopher full_name: Ahlbach, Christopher last_name: Ahlbach - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Haiyan full_name: Xu, Haiyan last_name: Xu - first_name: Owen L. full_name: Williams, Owen L. last_name: Williams - first_name: Tara L. full_name: Davis, Tara L. last_name: Davis - first_name: Andrew C. full_name: Liu, Andrew C. last_name: Liu - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Gustafson CL, Parsley NC, Asimgil H, et al. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. 2017;66(4):447-457.e7. doi:10.1016/j.molcel.2017.04.011 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. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2017.04.011 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.” Molecular Cell. Elsevier, 2017. https://doi.org/10.1016/j.molcel.2017.04.011. ieee: C. L. Gustafson et al., “A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms,” Molecular Cell, vol. 66, no. 4. Elsevier, p. 447–457.e7, 2017. 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.” Molecular Cell, vol. 66, no. 4, Elsevier, 2017, p. 447–457.e7, doi:10.1016/j.molcel.2017.04.011. 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. date_created: 2024-03-21T07:56:01Z date_published: 2017-05-18T00:00:00Z date_updated: 2024-03-25T12:19:20Z day: '18' doi: 10.1016/j.molcel.2017.04.011 extern: '1' fulldoi: https://doi.org/10.1016/j.molcel.2017.04.011 intvolume: ' 66' issue: '4' keyword: - Cell Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2017.04.011 month: '05' oa: 1 oa_version: Published Version page: 447-457.e7 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2017' ... --- _id: '15156' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Roger full_name: Tseng, Roger last_name: Tseng - first_name: Nicolette F. full_name: Goularte, Nicolette F. last_name: Goularte - first_name: Archana full_name: Chavan, Archana last_name: Chavan - first_name: Jansen full_name: Luu, Jansen last_name: Luu - first_name: Susan E. full_name: Cohen, Susan E. last_name: Cohen - first_name: Yong-Gang full_name: Chang, Yong-Gang last_name: Chang - first_name: Joel full_name: Heisler, Joel last_name: Heisler - first_name: Sheng full_name: Li, Sheng last_name: Li - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Sarvind full_name: Tripathi, Sarvind last_name: Tripathi - first_name: Susan S. full_name: Golden, Susan S. last_name: Golden - first_name: Andy full_name: LiWang, Andy last_name: LiWang - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition in a bacterial circadian clock. Science. 2017;355(6330):1174-1180. doi:10.1126/science.aag2516 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. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag2516 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.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2516. ieee: R. Tseng et al., “Structural basis of the day-night transition in a bacterial circadian clock,” Science, vol. 355, no. 6330. American Association for the Advancement of Science, pp. 1174–1180, 2017. 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. mla: Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” Science, vol. 355, no. 6330, American Association for the Advancement of Science, 2017, pp. 1174–80, doi:10.1126/science.aag2516. 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. date_created: 2024-03-21T07:56:24Z date_published: 2017-03-17T00:00:00Z date_updated: 2024-03-25T12:16:44Z day: '17' doi: 10.1126/science.aag2516 extern: '1' fulldoi: https://doi.org/10.1126/science.aag2516 intvolume: ' 355' issue: '6330' keyword: - Multidisciplinary language: - iso: eng month: '03' oa_version: None page: 1174-1180 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of the day-night transition in a bacterial circadian clock type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 355 year: '2017' ... --- _id: '15157' 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. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Jennifer L. full_name: Fribourgh, Jennifer L. last_name: Fribourgh - first_name: Yogarany full_name: Chelliah, Yogarany last_name: Chelliah - first_name: Colby R. full_name: Sandate, Colby R. last_name: Sandate - first_name: Greg L. full_name: Hura, Greg L. last_name: Hura - first_name: Dina full_name: Schneidman-Duhovny, Dina last_name: Schneidman-Duhovny - first_name: Sarvind M. full_name: Tripathi, Sarvind M. last_name: Tripathi - first_name: Joseph S. full_name: Takahashi, Joseph S. last_name: Takahashi - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: 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. Proceedings of the National Academy of Sciences. 2017;114(7):1560-1565. doi:10.1073/pnas.1615310114 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. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1615310114 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.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1615310114. ieee: A. K. Michael et al., “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, vol. 114, no. 7. Proceedings of the National Academy of Sciences, pp. 1560–1565, 2017. 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.” Proceedings of the National Academy of Sciences, vol. 114, no. 7, Proceedings of the National Academy of Sciences, 2017, pp. 1560–65, doi:10.1073/pnas.1615310114. 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. date_created: 2024-03-21T07:56:50Z date_published: 2017-01-31T00:00:00Z date_updated: 2024-03-25T12:12:23Z day: '31' doi: 10.1073/pnas.1615310114 extern: '1' external_id: pmid: - '28143926' fulldoi: https://doi.org/10.1073/pnas.1615310114 intvolume: ' 114' issue: '7' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1615310114 month: '01' oa: 1 oa_version: Published Version page: 1560-1565 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '15158' abstract: - lang: eng 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: Drosophila‐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.' article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Jennifer L. full_name: Fribourgh, Jennifer L. last_name: Fribourgh - first_name: Russell N. full_name: Van Gelder, Russell N. last_name: Van Gelder - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: 'Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. 2017;93(1):128-140. doi:10.1111/php.12677' apa: 'Michael, A. K., Fribourgh, J. L., Van Gelder, R. N., & Partch, C. L. (2017). Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry and Photobiology. Wiley. https://doi.org/10.1111/php.12677' 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.” Photochemistry and Photobiology. Wiley, 2017. https://doi.org/10.1111/php.12677.' 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,” Photochemistry and Photobiology, vol. 93, no. 1. Wiley, pp. 128–140, 2017.' 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.” Photochemistry and Photobiology, vol. 93, no. 1, Wiley, 2017, pp. 128–40, doi:10.1111/php.12677.' short: A.K. Michael, J.L. Fribourgh, R.N. Van Gelder, C.L. Partch, Photochemistry and Photobiology 93 (2017) 128–140. date_created: 2024-03-21T07:57:18Z date_published: 2017-02-01T00:00:00Z date_updated: 2024-03-25T12:09:21Z day: '01' doi: 10.1111/php.12677 extern: '1' fulldoi: https://doi.org/10.1111/php.12677 intvolume: ' 93' issue: '1' keyword: - Physical and Theoretical Chemistry - General Medicine - Biochemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/php.12677 month: '02' oa: 1 oa_version: Published Version page: 128-140 publication: Photochemistry and Photobiology publication_identifier: eissn: - 1751-1097 issn: - 0031-8655 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Animal cryptochromes: Divergent roles in light perception, circadian timekeeping and beyond' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2017' ... --- _id: '15159' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Hande full_name: Asimgil, Hande last_name: Asimgil - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006 apa: Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006 chicago: Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006. ieee: A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015. 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.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006. short: A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490. date_created: 2024-03-21T07:57:44Z date_published: 2015-09-01T00:00:00Z date_updated: 2024-03-25T11:53:58Z day: '01' doi: 10.1016/j.tibs.2015.07.006 extern: '1' fulldoi: https://doi.org/10.1016/j.tibs.2015.07.006 intvolume: ' 40' issue: '9' keyword: - Molecular Biology - Biochemistry language: - iso: eng month: '09' oa_version: None page: 489-490 publication: Trends in Biochemical Sciences publication_identifier: issn: - 0968-0004 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cytosolic BMAL1 moonlights as a translation factor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2015' ... --- _id: '15160' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Stacy L. full_name: Harvey, Stacy L. last_name: Harvey - first_name: Patrick J. full_name: Sammons, Patrick J. last_name: Sammons - first_name: Amanda P. full_name: Anderson, Amanda P. last_name: Anderson - first_name: Hema M. full_name: Kopalle, Hema M. last_name: Kopalle - first_name: Alison H. full_name: Banham, Alison H. last_name: Banham - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031 apa: Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031 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.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031. ieee: A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015. 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.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031. 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. date_created: 2024-03-21T07:58:08Z date_published: 2015-06-04T00:00:00Z date_updated: 2024-03-25T11:52:26Z day: '04' doi: 10.1016/j.molcel.2015.03.031 extern: '1' fulldoi: https://doi.org/10.1016/j.molcel.2015.03.031 intvolume: ' 58' issue: '5' keyword: - Cell Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2015.03.031 month: '06' oa: 1 oa_version: Published Version page: 743-754 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cancer/Testis antigen PASD1 silences the circadian clock type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2015' ... --- _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. article_processing_charge: No article_type: letter_note author: - first_name: Weiye full_name: Guan, Weiye last_name: Guan - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Melissa L. full_name: McIntosh, Melissa L. last_name: McIntosh - first_name: Liza full_name: Koren-Selfridge, Liza last_name: Koren-Selfridge - first_name: John P. full_name: Scott, John P. last_name: Scott - first_name: Timothy B. full_name: Clark, Timothy B. last_name: Clark citation: 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. The Journal of Organic Chemistry. 2014;79(15):7199-7204. doi:10.1021/jo500773t apa: Guan, W., Michael, A. K., McIntosh, M. L., Koren-Selfridge, L., Scott, J. P., & Clark, T. B. (2014). Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/jo500773t 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.” The Journal of Organic Chemistry. American Chemical Society, 2014. https://doi.org/10.1021/jo500773t. 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,” The Journal of Organic Chemistry, vol. 79, no. 15. American Chemical Society, pp. 7199–7204, 2014. 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. mla: Guan, Weiye, et al. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal of Organic Chemistry, vol. 79, no. 15, American Chemical Society, 2014, pp. 7199–204, doi:10.1021/jo500773t. 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. date_created: 2024-03-21T07:58:31Z date_published: 2014-06-10T00:00:00Z date_updated: 2024-03-25T11:50:01Z day: '10' doi: 10.1021/jo500773t extern: '1' fulldoi: https://doi.org/10.1021/jo500773t intvolume: ' 79' issue: '15' keyword: - Organic Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jo500773t month: '06' oa: 1 oa_version: Published Version page: 7199-7204 publication: The Journal of Organic Chemistry publication_identifier: eissn: - 1520-6904 issn: - 0022-3263 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2014' ...