@Article{Richter:Schleberger:Backofen:Seed_INTAR_predi:2010,
  author =	 {Richter, Andreas S. and Schleberger, Christian and 
                  Backofen, Rolf and Steglich, Claudia},
  title =	 {Seed-based {IntaRNA} prediction combined with 
                  {GFP}-reporter system identifies {mRNA} targets of the small 
                  {RNA} {Yfr1}},
  journal =	 {Bioinformatics},
  year =	 {2010},
  volume =	 {26},
  number =	 {1},
  pages =	 {1-5},
  user =	 {arichter},
  pmid =	 {19850757},
  doi = 	 {10.1093/bioinformatics/btp609},
  issn =	 {1367-4803},
  issn =	 {1460-2059},
  abstract =	 {MOTIVATION: Prochlorococcus possesses the smallest genome 
                  of all sequenced photoautotrophs. Although the number of 
                  regulatory proteins in the genome is very small, the 
                  relative number of small regulatory RNAs is comparable with 
                  that of other bacteria. The compact genome size of 
                  Prochlorococcus offers an ideal system to search for targets 
                  of small RNAs (sRNAs) and to refine existing target 
                  prediction algorithms. RESULTS: Target predictions for the 
                  cyanobacterial sRNA Yfr1 were carried out with INTARNA in 
                  Prochlorococcus MED4. The ultraconserved Yfr1 sequence motif 
                  was defined as the putative interaction seed. To study the 
                  impact of Yfr1 on its predicted mRNA targets, a reporter 
                  system based on green fluorescent protein (GFP) was applied. 
                  We show that Yfr1 inhibits the translation of two predicted 
                  targets. We used mutation analysis to confirm that Yfr1 
                  directly regulates its targets by an antisense interaction 
                  sequestering the ribosome binding site, and to assess the 
                  importance of interaction site accessibility.}
}