{"abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"corr_author":"1","citation":{"ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. <i>Coevolution of Transcription Factors and Their Binding Sites in Sequence Space</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>.","apa":"Prizak, R. (2019). <i>Coevolution of transcription factors and their binding sites in sequence space</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>."},"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"1358","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"955","relation":"part_of_dissertation"}]},"file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2019-03-06T16:05:07Z","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_updated":"2020-07-14T12:47:18Z","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","creator":"rprizak","file_id":"6072","file_size":20995465,"relation":"main_file"},{"relation":"source_file","file_size":85705272,"file_name":"thesis_v2_merge.zip","creator":"rprizak","file_id":"6073","access_level":"closed","title":"Latex files","content_type":"application/zip","checksum":"67c2630333d05ebafef5f018863a8465","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z"}],"has_accepted_license":"1","title":"Coevolution of transcription factors and their binding sites in sequence space","date_updated":"2024-12-10T11:14:05Z","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"}],"alternative_title":["ISTA Thesis"],"ddc":["576"],"oa_version":"Published Version","supervisor":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"type":"dissertation","_id":"6071","date_published":"2019-03-11T00:00:00Z","degree_awarded":"PhD","month":"03","year":"2019","file_date_updated":"2020-07-14T12:47:18Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"doi":"10.15479/at:ista:th6071","oa":1,"date_created":"2019-03-06T16:16:10Z","page":"189"}