---
OA_place: publisher
_id: '19431'
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."
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.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Annamaria
  full_name: Hlavata, Annamaria
  id: 36062FEC-F248-11E8-B48F-1D18A9856A87
  last_name: Hlavata
citation:
  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>
  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>.
  ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science
    and Technology Austria, 2025.
  ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of
    Science and Technology Austria.
  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>.
  short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science
    and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-20T12:52:47Z
date_published: 2025-03-20T00:00:00Z
date_updated: 2026-04-07T11:46:32Z
day: '20'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaBe
doi: 10.15479/10.15479/AT-ISTA-19431
file:
- access_level: closed
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  creator: ahlavata
  date_created: 2025-03-24T12:48:36Z
  date_updated: 2026-03-20T23:30:04Z
  embargo_to: open_access
  file_id: '19448'
  file_name: PhD_Thesis_Hlavata_final_submission.docx
  file_size: 23506747
  relation: source_file
- access_level: open_access
  checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4
  content_type: application/pdf
  creator: ahlavata
  date_created: 2025-03-24T12:51:10Z
  date_updated: 2026-03-20T23:30:04Z
  embargo: 2026-03-20
  file_id: '19449'
  file_name: PhD_Thesis_Hlavata_final_submission_update.pdf
  file_size: 9478591
  relation: main_file
file_date_updated: 2026-03-20T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
  eissn:
  - 2663-337X
  isbn:
  - 978-3-99078-055-8
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carrie A
  full_name: Bernecky, Carrie A
  id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
  last_name: Bernecky
  orcid: 0000-0003-0893-7036
title: Regulation of Cytoplasmic RNA Polymerase II
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...