{"project":[{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"volume":31,"has_accepted_license":"1","article_type":"original","intvolume":"        31","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"date_updated":"2023-02-13T09:20:34Z","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"}],"status":"public","day":"01","quality_controlled":"1","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. ","publisher":"Elsevier","oa":1,"scopus_import":"1","publication_status":"published","_id":"12156","doi":"10.1016/j.coisb.2022.100435","publication_identifier":{"issn":["2452-3100"]},"title":"Eukaryotic gene regulation at equilibrium, or non?","issue":"9","month":"09","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"oa_version":"Published Version","citation":{"apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435."},"type":"journal_article","publication":"Current Opinion in Systems Biology","article_number":"100435","date_created":"2023-01-12T12:08:51Z","ddc":["570"],"year":"2022","file":[{"relation":"main_file","date_updated":"2023-01-24T12:14:10Z","content_type":"application/pdf","file_size":2214944,"file_name":"2022_CurrentBiology_Zoller.pdf","date_created":"2023-01-24T12:14:10Z","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","creator":"dernst","file_id":"12362","access_level":"open_access","success":1}],"article_processing_charge":"Yes (via OA deal)","date_published":"2022-09-01T00:00:00Z","file_date_updated":"2023-01-24T12:14:10Z","language":[{"iso":"eng"}],"author":[{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"},{"orcid":"1","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}]}