{"abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"issue":"11","date_published":"2015-11-06T00:00:00Z","publication_status":"published","date_updated":"2023-09-07T11:53:49Z","tmp":{"image":"/images/cc_by.png","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"},"month":"11","day":"06","type":"journal_article","file":[{"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","relation":"main_file","file_id":"4657","date_created":"2018-12-12T10:07:58Z","file_size":2580778,"date_updated":"2020-07-14T12:45:10Z"}],"status":"public","related_material":{"record":[{"status":"public","id":"9712","relation":"research_data"},{"status":"public","id":"1131","relation":"dissertation_contains"}]},"quality_controlled":"1","title":"Dynamics of transcription factor binding site evolution","scopus_import":1,"publisher":"Public Library of Science","date_created":"2018-12-11T11:53:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","oa":1,"_id":"1666","pubrep_id":"463","language":[{"iso":"eng"}],"citation":{"short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>."},"ec_funded":1,"has_accepted_license":"1","author":[{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","last_name":"Tugrul"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1005639","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"ddc":["576"],"file_date_updated":"2020-07-14T12:45:10Z","year":"2015","volume":11,"publist_id":"5483","intvolume":"        11"}