{"type":"journal_article","keyword":["Genetics and Molecular Biology"],"author":[{"orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin"},{"last_name":"Caruso Carter","first_name":"Caroline","full_name":"Caruso Carter, Caroline"},{"full_name":"Sonnleitner, Elisabeth","first_name":"Elisabeth","last_name":"Sonnleitner"},{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X"},{"first_name":"Tiago","last_name":"Paixão","full_name":"Paixão, Tiago"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"related_material":{"record":[{"relation":"research_data","id":"8951","status":"public"}]},"publication_identifier":{"issn":["2050-084X"]},"intvolume":"        10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-03-08T00:00:00Z","date_updated":"2024-02-21T12:41:57Z","quality_controlled":"1","publication_status":"published","article_processing_charge":"Yes","day":"08","has_accepted_license":"1","article_number":"e65993","isi":1,"date_created":"2021-03-23T10:11:46Z","language":[{"iso":"eng"}],"acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.","lang":"eng"}],"file":[{"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","access_level":"open_access","relation":"main_file","success":1,"content_type":"application/pdf","file_name":"elife-65993-v2.pdf","file_id":"9284","date_created":"2021-03-23T10:12:58Z","file_size":1390469,"date_updated":"2021-03-23T10:12:58Z","creator":"bkavcic"}],"doi":"10.7554/elife.65993","file_date_updated":"2021-03-23T10:12:58Z","publisher":"eLife Sciences Publications","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Local genetic context shapes the function of a gene regulatory network","external_id":{"isi":["000631050900001"]},"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"month":"03","citation":{"short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>.","ieee":"A. A. Nagy-Staron <i>et al.</i>, “Local genetic context shapes the function of a gene regulatory network,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>, vol. 10, e65993, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>.","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &#38; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>"},"_id":"9283","year":"2021","article_type":"original","volume":10,"project":[{"name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","_id":"2517526A-B435-11E9-9278-68D0E5697425","grant_number":"628377","call_identifier":"FP7"},{"_id":"268BFA92-B435-11E9-9278-68D0E5697425","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","call_identifier":"FWF","grant_number":"I03901"}],"ddc":["570"],"publication":"eLife","ec_funded":1,"status":"public","oa_version":"Published Version"}