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Mapping the small RNA interactome in bacteria using RIL-seq

Abstract

Small RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA–target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental–computational methodology for capturing sRNA–target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing. The computational pipeline maps the sequenced fragments to the genome, reveals chimeric fragments (fragments comprising two ligated independent fragments) and determines statistically significant overrepresented chimeric fragments as interacting RNAs. The statistical filter is aimed at reducing the number of spurious interactions resulting from ligation of random neighboring RNA fragments, thus increasing the reliability of the determined sRNA–target pairs. A major advantage of RIL-seq is that it does not require overexpression of sRNAs; instead, it simultaneously captures the in vivo targets of all sRNAs in the native state of the cell. Application of RIL-seq to bacteria grown under different conditions provides distinctive snapshots of the sRNA interactome and sheds light on the dynamics and rewiring of the post-transcriptional regulatory network. As RIL-seq needs no prior information about the sRNA and target sequences, it can identify novel sRNAs, along with their targets. It can be adapted to detect protein-mediated RNA–RNA interactions in any bacterium with a sequenced genome. The experimental part of the RIL-seq protocol takes 7–9 d and the computational analysis takes 2 d.

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Figure 1: Overview of RIL-seq experimental and computational procedures.
Figure 2: The configuration of DNA fragments in the sequencing library.
Figure 3: Flow chart of the computational analysis.
Figure 4: Typical Bioanalyzer electropherograms showing the RNA profile at different steps of the protocol.
Figure 5: TapeStation electropherograms.
Figure 6: Schematic representation of the S-chimera coordinates reported in the output file (Supplementary Table 1).

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Acknowledgements

This study was supported by European Research Council Advanced Grant 322920, the I-CORE Programs of the Planning and Budgeting Committee and The Israel Science Foundation (grants 1796/12 and 41/1), and the Israel Science Foundation, administered by the Israeli Academy for Sciences and Humanities (grant 1411/13). We thank Y. Gatt, S. Pearl-Mizrahi, A. Zhang and H. Zhang for their useful comments.

Author information

Authors and Affiliations

Authors

Contributions

H.M. guided the study. S.M. and A.P. developed the methodology; S.M., R.F.-R. and L.A. carried out the experiments.; A.P., Y.A. and R.F.-R. curated the data; A.P. developed the software; A.P., Y.A., R.F.-R., N.R. and A.B. carried out the computational analyses; N.R., O.S. and A.B. updated and tested the software. S.M., A.P., Y.A., L.A., R.F.-R. and H.M. wrote the paper.

Corresponding authors

Correspondence to Yael Altuvia, Liron Argaman or Hanah Margalit.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 IP assay of crosslinked (CL) and non-crosslinked (nCL) Hfq-Flag

hfq-Flag and hfq-WT strains were grown to log phase, the cells were exposed to UV irradiation in order to generate protein-RNA crosslinking or unexposed, and cell lysates were prepared. The lysates were subjected to IP assay using magnetic beads carrying M2 anti-Flag monoclonal antibody. The lysates, unbound fraction and bound fraction (IP) were analyzed by Western blotting using Anti-Flag antibody. As a control for the IP assay, we incubated hfq-Flag lysate, without crosslinking, with magnetic beads carrying no M2 Anti-Flag antibody (Beads only).

* Bands of M2 anti-Flag monoclonal antibody light (bottom) and heavy (middle) chains in the IP lanes.

The figure is reprinted with permission from Melamed et al. 11

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1. (PDF 197 kb)

Supplementary Table 1

RIL-seq reports the list of S-chimeras in a tab-delimited table. (XLSX 11 kb)

Supplementary Table 2

Number of fragments in RIL-seq sequencing libraries.xls (XLSX 13 kb)

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Melamed, S., Faigenbaum-Romm, R., Peer, A. et al. Mapping the small RNA interactome in bacteria using RIL-seq. Nat Protoc 13, 1–33 (2018). https://doi.org/10.1038/nprot.2017.115

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