In vivo cleavage rules and target repertoire of RNase III in Escherichia coli
A transcriptome-wide computational approach for finding novel protein-RNA interactions.
Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3′ overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.
Citation
@article{altuvia2018vivo,
title={In vivo cleavage rules and target repertoire of RNase III in Escherichia coli},
author={Altuvia, Yael and Bar, Amir and Reiss, Niv and Karavani, Ehud and Argaman, Liron and Margalit, Hanah},
journal={Nucleic acids research},
volume={46},
number={19},
pages={10380--10394},
year={2018},
publisher={Oxford University Press}
}