@article{YeAmbiOlguinNavaetal.2021,
  author    = {Ye, Liqing and Ambi, Uddhav B. and Olguin-Nava, Marco and Gribling-Burrer, Anne-Sophie and Ahmad, Shazeb and Bohn, Patrick and Weber, Melanie M. and Smyth, Redmond P.},
  title     = {RNA structures and their role in selective genome packaging},
  series = {Viruses},
  volume    = {13},
  journal   = {Viruses},
  number    = {9},
  issn      = {1999-4915},
  doi       = {10.3390/v13091788},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-246101},
  year      = {2021},
  abstract  = {To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.},
  language  = {en}
}
@article{LioliouSharmaCaldelarietal.2012,
  author    = {Lioliou, Efthimia and Sharma, Cynthia M. and Caldelari, Isabelle and Helfer, Anne-Catherine and Fechter, Pierre and Vandenesch, Fran{\c{c}}ois and Vogel, J{\"o}rg and Romby, Pascale},
  title     = {Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression},
  series = {PLoS Genetics},
  volume    = {8},
  journal   = {PLoS Genetics},
  number    = {6},
  doi       = {10.1371/journal.pgen.1002782},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127219},
  pages     = {e1002782},
  year      = {2012},
  abstract  = {RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III-mediated cleavage in the 5′ untranslated region (5′UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5′UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44\% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III.},
  language  = {en}
}
@article{BodemSchromMoschalletal.2013,
  author    = {Bodem, Jochen and Schrom, Eva-Maria and Moschall, Rebecca and Hartl, Maximilian J. and Weitner, Helena and Fecher, David and Langemeier, J{\"o}rg and W{\"o}hrl, Brigitta M.},
  title     = {U1snRNP-mediated suppression of polyadenylation in conjunction with the RNA structure controls poly (A) site selection in foamy viruses},
  series = {Retrovirology},
  journal   = {Retrovirology},
  doi       = {10.1186/1742-4690-10-55},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96085},
  year      = {2013},
  abstract  = {Background During reverse transcription, retroviruses duplicate the long terminal repeats (LTRs). These identical LTRs carry both promoter regions and functional polyadenylation sites. To express full-length transcripts, retroviruses have to suppress polyadenylation in the 5′LTR and activate polyadenylation in the 3′LTR. Foamy viruses have a unique LTR structure with respect to the location of the major splice donor (MSD), which is located upstream of the polyadenylation signal. Results Here, we describe the mechanisms of foamy viruses regulating polyadenylation. We show that binding of the U1 small nuclear ribonucleoprotein (U1snRNP) to the MSD suppresses polyadenylation at the 5′LTR. In contrast, polyadenylation at the 3′LTR is achieved by adoption of a different RNA structure at the MSD region, which blocks U1snRNP binding and furthers RNA cleavage and subsequent polyadenylation. Conclusion Recently, it was shown that U1snRNP is able to suppress the usage of intronic cryptic polyadenylation sites in the cellular genome. Foamy viruses take advantage of this surveillance mechanism to suppress premature polyadenylation at the 5'end of their RNA. At the 3'end, Foamy viruses use a secondary structure to presumably block access of U1snRNP and thereby activate polyadenylation at the end of the genome. Our data reveal a contribution of U1snRNP to cellular polyadenylation site selection and to the regulation of gene expression.},
  subject      = {Polyadenylierung},
  language  = {en}
}