@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},
doi = {10.1093/nar/gkab1161},
volume = {49},
user = {backofen},
pmid = {34871439},
pages = {13075-13091},
number = {22},
issn = {0305-1048},
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.}
}