[{"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"abstract":[{"lang":"eng","text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm."}],"month":"03","file_date_updated":"2026-03-20T23:30:04Z","year":"2025","OA_place":"publisher","_id":"19431","date_updated":"2026-04-07T11:46:32Z","file":[{"file_name":"PhD_Thesis_Hlavata_final_submission.docx","access_level":"closed","date_updated":"2026-03-20T23:30:04Z","date_created":"2025-03-24T12:48:36Z","relation":"source_file","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","embargo_to":"open_access","file_size":23506747,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19448","creator":"ahlavata"},{"access_level":"open_access","date_updated":"2026-03-20T23:30:04Z","file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","embargo":"2026-03-20","file_size":9478591,"file_id":"19449","creator":"ahlavata","content_type":"application/pdf","relation":"main_file","date_created":"2025-03-24T12:51:10Z","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4"}],"author":[{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata","first_name":"Annamaria","full_name":"Hlavata, Annamaria"}],"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","day":"20","oa_version":"Published Version","doi":"10.15479/10.15479/AT-ISTA-19431","date_published":"2025-03-20T00:00:00Z","title":"Regulation of Cytoplasmic RNA Polymerase II","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-055-8"],"eissn":["2663-337X"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","article_processing_charge":"No","type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2025-03-20T12:52:47Z","has_accepted_license":"1","ddc":["572"],"page":"83","oa":1,"alternative_title":["ISTA Thesis"],"citation":{"apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>","chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>.","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025.","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025."},"supervisor":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036"}],"language":[{"iso":"eng"}],"publication_status":"published"}]