@PhdThesis{dbt_mods_00067820,
  author = 	{Lippegaus, Anne},
  title = 	{RNA networks controlling collective behaviors in Vibrio cholerae},
  year = 	{2025},
  address = 	{Jena},
  keywords = 	{RNS; Small RNA; Vibrio cholerae; Virulenz},
  abstract = 	{Small RNAs (sRNAs) are non-coding RNAs, that often interact with messenger RNAs (mRNAs) to modulate gene expression. RNA-binding proteins (RBPs) are crucial for stabilizing these interactions. Advances in RNA sequencing (RNA-seq) technologies have enabled the high-throughput characterization of RNA interaction partners, providing insights into RNA networks on a transcriptome-wide scale. Global methods, such as RIL-seq (RNA interaction by ligation and sequencing), have been developed to study RNA interactomes in vivo. This study employs RIL-seq with Hfq in Vibrio cholerae at low cell density (LCD) and high cell density (HCD). Thereby we identified 2,889 statistically significant RNA-RNA interactions. A deeper analysis revealed a previously uncharacterized RNA sponge, QrrX, which specifically interacts with the Quorum regulatory RNAs 1-4 (Qrr1-4). Moreover, this study presents an interactive RIL-seq browser to facilitate the identification of chimeric RNA molecules, derived from high-throughput methods. Among our findings, we identified two novel sRNAs, NetX and NetY (network-derived sRNAs X and Y), and demonstrated that NetX is a previously unrecognized regulator of virulence gene expression in V. cholerae. Furthermore, we investigated post-transcriptional regulation of virulence factors in V. cholerae. RNA-seq and RIL-seq analyses were conducted under virulence-inducing conditions, leading to the identification of a novel virulence-related sRNA. We named this sRNA CisR (CTX$\phi$ inhibiting sRNA) due to its regulatory effect on the cep mRNA, which is encoded by the filamentous bacteriophage CTX$\phi$. Collectively, the findings presented in this thesis reveal the complexity of the sRNA landscape in V. cholerae and provides an interactive visualization of RNA interactomes in V. cholerae under both standard laboratory conditions and virulence inducing conditions and thus lays the foundation for discovering new mechanisms of RNA-based regulation.},
  note = 	{Dissertation, Friedrich-Schiller-Universit{\"a}t Jena, 2025},
  doi = 	{10.22032/dbt.67820},
  url = 	{https://www.db-thueringen.de/receive/dbt_mods_00067820},
  url = 	{http://uri.gbv.de/document/gvk:ppn:1939392470},
  url = 	{https://doi.org/10.22032/dbt.67820},
  file = 	{:https://www.db-thueringen.de/servlets/MCRFileNodeServlet/dbt_derivate_00069271/Dissertation_AnneLippegaus.pdf:PDF},
  language = 	{en}
}