title: Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays.
abstract: RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis. Its characterization provided the first evidence that endonucleolytic cleavage plays a major role in the mRNA metabolism of this organism. RNase Y shares important functional features with the RNA decay initiating RNase E from Escherichia coli, notably a similar cleavage specificity and a preference for 5' monophosphorylated substrates. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. The downstream cleavage products are likely to be degraded by the 5' exonucleolytic activity of RNases J1/J2 as we show for a specific case. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% were in common in all three studies. This highlights that experimental conditions and data analysis play an important role in identifying RNase Y substrates by global transcriptional profiling. Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allow an exceptionally detailed view of the turnover of hundreds of new RNA substrates.
authors: CNRS UPR 9073 (affiliated with University Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France.
authors: Soumaya
authors: S
authors: Laalami
authors: Philippe
authors: P
authors: Bessières
authors: Anna
authors: A
authors: Rocca
authors: Léna
authors: L
authors: Zig
authors: Pierre
authors: P
authors: Nicolas
authors: Harald
authors: H
authors: Putzer
mesh_terms: D001412:Bacillus subtilis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D004722:Endoribonucleases / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D012260:Ribonucleases / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D004722:Endoribonucleases; D012260:Ribonucleases; C022537:ribonuclease E