@Article{Hoffmann_Heyl_Rogh-Trans_vivo_mappi-NAR2021,
  author =	 {Hoffmann, Ute A. and Heyl, Florian and Rogh, Said N. and 
                  Wallner, Thomas and Backofen, Rolf and Hess, Wolfgang R. and 
                  Steglich, Claudia and Wilde, Annegret},
  title =	 {Transcriptome-wide in vivo mapping of cleavage sites for 
                  the compact cyanobacterial ribonuclease {E} reveals insights 
                  into its function and substrate recognition},
  journal =	 NAR,
  year =	 {2021},
  volume =	 {49},
  number =	 {22},
  pages =	 {13075-13091},
  user =	 {backofen},
  pmid =	 {34871439},
  doi = 	 {10.1093/nar/gkab1161},
  issn = 	 {0305-1048},
  issn = 	 {1362-4962},
  abstract =	 {Ribonucleases are crucial enzymes in RNA metabolism and 
                  post-transcriptional regulatory processes in bacteria. 
                  Cyanobacteria encode the two essential ribonucleases RNase E 
                  and RNase J. Cyanobacterial RNase E is shorter than 
                  homologues in other groups of bacteria and lacks both the 
                  chloroplast-specific N-terminal extension as well as the 
                  C-terminal domain typical for RNase E of enterobacteria. In 
                  order to investigate the function of RNase E in the model 
                  cyanobacterium Synechocystis sp. PCC 6803, we engineered a 
                  temperature-sensitive RNase E mutant by introducing two 
                  site-specific mutations, I65F and the spontaneously occurred 
                  V94A. This enabled us to perform RNA-seq after the transient 
                  inactivation of RNase E by a temperature shift (TIER-seq) 
                  and to map 1472 RNase-E-dependent cleavage sites. We 
                  inferred a dominating cleavage signature consisting of an 
                  adenine at the -3 and a uridine at the +2 position within a 
                  single-stranded segment of the RNA. The data identified 
                  mRNAs likely regulated jointly by RNase E and an sRNA and 
                  potential 3' end-derived sRNAs. Our findings substantiate 
                  the pivotal role of RNase E in post-transcriptional 
                  regulation and suggest the redundant or concerted action of 
                  RNase E and RNase J in cyanobacteria.}
}