@article{WhisnantJuergesHennigetal.2020,
  author    = {Whisnant, Adam W. and J{\"u}rges, Christopher S. and Hennig, Thomas and Wyler, Emanuel and Prusty, Bhupesh and Rutkowski, Andrzej J. and L'hernault, Anne and Djakovic, Lara and G{\"o}bel, Margarete and D{\"o}ring, Kristina and Menegatti, Jennifer and Antrobus, Robin and Matheson, Nicholas J. and K{\"u}nzig, Florian W. H. and Mastrobuoni, Guido and Bielow, Chris and Kempa, Stefan and Liang, Chunguang and Dandekar, Thomas and Zimmer, Ralf and Landthaler, Markus and Gr{\"a}sser, Friedrich and Lehner, Paul J. and Friedel, Caroline C. and Erhard, Florian and D{\"o}lken, Lars},
  title     = {Integrative functional genomics decodes herpes simplex virus 1},
  series = {Nature Communications},
  volume    = {11},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-020-15992-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229884},
  year      = {2020},
  abstract  = {The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.},
  language  = {en}
}
@article{MurakawaHinzMothesetal.2015,
  author    = {Murakawa, Yasuhiro and Hinz, Michael and Mothes, Janina and Schuetz, Anja and Uhl, Michael and Wyler, Emanuel and Yasuda, Tomoharu and Mastrobuoni, Guido and Friedel, Caroline C. and D{\"o}lken, Lars and Kempa, Stefan and Schmidt-Supprian, Marc and Bl{\"u}thgen, Nils and Backofen, Rolf and Heinemann, Udo and Wolf, Jana and Scheidereit, Claus and Landthaler, Markus},
  title     = {RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway},
  series = {Nature Communications},
  volume    = {6},
  journal   = {Nature Communications},
  number    = {7367},
  doi       = {10.1038/ncomms8367},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151596},
  year      = {2015},
  abstract  = {The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNF\(\alpha\) mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ~3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-\(\kappa\)B pathway regulators such as I\(\kappa\)B\(\alpha\) and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with I\(\kappa\)B kinase and NF-\(\kappa\)B activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-\(\kappa\)B pathway.},
  language  = {en}
}