[{"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","apa":"Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435."},"publication":"Current Opinion in Systems Biology","date_published":"2022-09-01T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"intvolume":" 31","title":"Eukaryotic gene regulation at equilibrium, or non?","ddc":["570"],"status":"public","_id":"12156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","success":1,"date_created":"2023-01-24T12:14:10Z","date_updated":"2023-01-24T12:14:10Z","relation":"main_file","file_id":"12362","file_size":2214944,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_CurrentBiology_Zoller.pdf"}],"oa_version":"Published Version","publication_identifier":{"issn":["2452-3100"]},"month":"09","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.coisb.2022.100435","article_number":"100435","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-01-24T12:14:10Z","publisher":"Elsevier","department":[{"_id":"GaTk"}],"publication_status":"published","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","year":"2022","volume":31,"date_created":"2023-01-12T12:08:51Z","date_updated":"2023-02-13T09:20:34Z","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1"}]},{"issue":"11","abstract":[{"lang":"eng","text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9018","intvolume":" 26","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","status":"public","article_processing_charge":"No","day":"21","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"date_published":"2019-11-21T00:00:00Z","citation":{"ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002."},"publication":"Cell Chemical Biology","page":"1573-1585.e10","article_type":"original","extern":"1","author":[{"full_name":"Bakail, May M","first_name":"May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587"},{"last_name":"Gaubert","first_name":"Albane","full_name":"Gaubert, Albane"},{"first_name":"Jessica","last_name":"Andreani","full_name":"Andreani, Jessica"},{"full_name":"Moal, Gwenaëlle","last_name":"Moal","first_name":"Gwenaëlle"},{"last_name":"Pinna","first_name":"Guillaume","full_name":"Pinna, Guillaume"},{"full_name":"Boyarchuk, Ekaterina","first_name":"Ekaterina","last_name":"Boyarchuk"},{"full_name":"Gaillard, Marie-Cécile","first_name":"Marie-Cécile","last_name":"Gaillard"},{"full_name":"Courbeyrette, Regis","first_name":"Regis","last_name":"Courbeyrette"},{"first_name":"Carl","last_name":"Mann","full_name":"Mann, Carl"},{"full_name":"Thuret, Jean-Yves","last_name":"Thuret","first_name":"Jean-Yves"},{"full_name":"Guichard, Bérengère","last_name":"Guichard","first_name":"Bérengère"},{"last_name":"Murciano","first_name":"Brice","full_name":"Murciano, Brice"},{"full_name":"Richet, Nicolas","first_name":"Nicolas","last_name":"Richet"},{"full_name":"Poitou, Adeline","last_name":"Poitou","first_name":"Adeline"},{"last_name":"Frederic","first_name":"Claire","full_name":"Frederic, Claire"},{"full_name":"Le Du, Marie-Hélène","last_name":"Le Du","first_name":"Marie-Hélène"},{"full_name":"Agez, Morgane","last_name":"Agez","first_name":"Morgane"},{"full_name":"Roelants, Caroline","last_name":"Roelants","first_name":"Caroline"},{"full_name":"Gurard-Levin, Zachary A.","last_name":"Gurard-Levin","first_name":"Zachary A."},{"full_name":"Almouzni, Geneviève","last_name":"Almouzni","first_name":"Geneviève"},{"full_name":"Cherradi, Nadia","first_name":"Nadia","last_name":"Cherradi"},{"first_name":"Raphael","last_name":"Guerois","full_name":"Guerois, Raphael"},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"}],"volume":26,"date_updated":"2023-02-23T13:46:53Z","date_created":"2021-01-19T11:04:50Z","pmid":1,"year":"2019","publisher":"Elsevier","publication_status":"published","publication_identifier":{"issn":["2451-9456"]},"month":"11","doi":"10.1016/j.chembiol.2019.09.002","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chembiol.2019.09.002"}],"external_id":{"pmid":["31543461"]},"oa":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1016/s0040-4020(03)00682-3","quality_controlled":"1","publication_identifier":{"eissn":["1464-5416"],"issn":["0040-4020"]},"month":"06","volume":59,"date_updated":"2023-08-08T12:44:17Z","date_created":"2023-08-01T10:39:34Z","author":[{"first_name":"Anna","last_name":"Michrowska","full_name":"Michrowska, Anna"},{"full_name":"Bieniek, Michał","last_name":"Bieniek","first_name":"Michał"},{"first_name":"Mikhail","last_name":"Kim","full_name":"Kim, Mikhail"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"},{"full_name":"Grela, Karol","first_name":"Karol","last_name":"Grela"}],"publisher":"Elsevier","publication_status":"published","year":"2003","extern":"1","date_published":"2003-06-16T00:00:00Z","page":"4525-4531","article_type":"original","citation":{"ama":"Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. 2003;59(25):4525-4531. doi:10.1016/s0040-4020(03)00682-3","ieee":"A. Michrowska, M. Bieniek, M. Kim, R. Klajn, and K. Grela, “Cross-metathesis reaction of vinyl sulfones and sulfoxides,” Tetrahedron, vol. 59, no. 25. Elsevier, pp. 4525–4531, 2003.","apa":"Michrowska, A., Bieniek, M., Kim, M., Klajn, R., & Grela, K. (2003). Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. Elsevier. https://doi.org/10.1016/s0040-4020(03)00682-3","ista":"Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. 2003. Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. 59(25), 4525–4531.","short":"A. Michrowska, M. Bieniek, M. Kim, R. Klajn, K. Grela, Tetrahedron 59 (2003) 4525–4531.","mla":"Michrowska, Anna, et al. “Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.” Tetrahedron, vol. 59, no. 25, Elsevier, 2003, pp. 4525–31, doi:10.1016/s0040-4020(03)00682-3.","chicago":"Michrowska, Anna, Michał Bieniek, Mikhail Kim, Rafal Klajn, and Karol Grela. “Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.” Tetrahedron. Elsevier, 2003. https://doi.org/10.1016/s0040-4020(03)00682-3."},"publication":"Tetrahedron","article_processing_charge":"No","day":"16","keyword":["Organic Chemistry","Drug Discovery","Biochemistry"],"scopus_import":"1","oa_version":"None","intvolume":" 59","title":"Cross-metathesis reaction of vinyl sulfones and sulfoxides","status":"public","_id":"13436","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"25","abstract":[{"lang":"eng","text":"Cross-metathesis reactions of α,β-unsaturated sulfones and sulfoxides in the presence of molybdenum and ruthenium pre-catalysts were tested. A selective metahesis reaction was achieved between functionalized terminal olefins and vinyl sulfones by using the ‘second generation’ ruthenium catalysts 1c–h while the highly active Schrock catalyst 1b was found to be functional group incompatible with vinyl sulfones. The cross-metathesis products were isolated in good yields with an excellent (E)-selectivity. Both the molybdenum and ruthenium-based complexes were, however, incompatible with α,β- and β,γ-unsaturated sulfoxides."}],"type":"journal_article"}]