@Article{Holmqvist_Wright_Li-Globa_RNA_recog-2016,
  author =	 {Holmqvist, Erik and Wright, Patrick R. and Li, Lei and 
                  Bischler, Thorsten and Barquist, Lars and Reinhardt, Richard 
                  and Backofen, Rolf and Vogel, Jorg},
  title =	 {Global {RNA} recognition patterns of post-transcriptional 
                  regulators {Hfq} and {CsrA} revealed by {UV} crosslinking in 
                  vivo},
  journal =	 {EMBO J},
  year =	 {2016},
  volume =	 {35},
  number =	 {9},
  pages =	 {991-1011},
  user =	 {wrightp},
  pmid =	 {27044921},
  doi = 	 {10.15252/embj.201593360},
  issn = 	 {0261-4189},
  issn = 	 {1460-2075},
  abstract =	 {The molecular roles of manyRNA-binding proteins in 
                  bacterial post-transcriptional gene regulation are not well 
                  understood. Approaches combiningin vivo UVcrosslinking 
                  withRNAdeep sequencing (CLIP-seq) have begun to 
                  revolutionize the transcriptome-wide mapping of 
                  eukaryoticRNA-binding protein target sites. We have 
                  appliedCLIP-seq to chart the target landscape of two major 
                  bacterial post-transcriptional regulators, Hfq and CsrA, in 
                  the model pathogenSalmonellaTyphimurium. By detecting 
                  binding sites at single-nucleotide resolution, we 
                  identifyRNApreferences and structural constraints of Hfq and 
                  CsrA during their interactions with hundreds of cellular 
                  transcripts. This reveals 3'-located Rho-independent 
                  terminators as a universal motif involved in 
                  Hfq-RNAinteractions. Additionally, Hfq preferentially binds 
                  5' tosRNA-target sites inmRNAs, and 3' to seed sequences 
                  insRNAs, reflecting a simple logic in how Hfq 
                  facilitatessRNA-mRNAinteractions. Importantly, global 
                  knowledge of Hfq sites significantly improvessRNA-target 
                  predictions. CsrA bindsAUGGAsequences in apical loops and 
                  targets manySalmonellavirulencemRNAs. Overall, our 
                  genericCLIP-seq approach will bring new insights into 
                  post-transcriptional gene regulation byRNA-binding proteins 
                  in diverse bacterial species.}
}