Multiple Approaches for the Investigation of Bacterial Small Regulatory RNAs Self-assembly

  • Christophe Lavelle
  • Florent Busi
  • Véronique Arluison
Part of the Methods in Molecular Biology book series (MIMB, volume 1297)

Abstract

RNAs are flexible molecules involved in a multitude of roles in the cell. Specifically, noncoding RNAs (i.e., RNAs that do not encode a protein) have important functions in the regulation of biological processes such as RNA decay, translation, or protein translocation. In bacteria, most of those noncoding RNAs have been shown to be critical for posttranscriptional control through their binding to the untranslated regions of target mRNAs. Recent evidence shows that some of these noncoding RNAs have the propensity to self-assemble in prokaryotes. Although the function of this self-assembly is not known and may vary from one RNA to another, it offers new insights into riboregulation pathways. We present here the various approaches that can be used for the detection and analysis of bacterial small noncoding RNA self-assemblies.

Key words

Small noncoding RNA Posttranscriptional control Nucleic acid self-assembly RNA nanostructure 

Abbreviations

AFM

Atomic force microscopy

bp

Base pair

FTIR

Fourier transform infrared spectroscopy

ncRNA

Noncoding RNA

nt

Nucleotide

PAGE

Polyacrylamide gel electrophoresis

RNAP

RNA polymerase

ss/ds RNA

Single- or double-stranded RNA

sRNA

Small regulatory RNA

TEM

Transmission electron microscopy

Tm

Melting temperature

Notes

Acknowledgements

This work was supported by the CNRS, CEA, and University Paris Diderot. We are particularly grateful to B. Cayrol (Leon Brillouin and AGAP Labs.), F. Geinguenaud (U. Paris 13), J. Teixeira (Leon Brillouin Lab), Olivier Piétrement (Gustave Roussy Institute and U. Paris 11), G. Wegrzyn (U. of Gdansk, Poland), Anthony Bugaut (National Museum of Natural History, Paris), and N. Linder (U. of Cergy-Pontoise) for their help in preparing this manuscript or for its critical reading.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Christophe Lavelle
    • 1
    • 2
  • Florent Busi
    • 3
    • 4
  • Véronique Arluison
    • 2
    • 3
    • 5
  1. 1.National Museum of Natural HistoryCNRS UMR7196/INSERM U1154ParisFrance
  2. 2.Nuclear Architecture and DynamicsCNRS GDR3536ParisFrance
  3. 3.Univ Paris Diderot-Paris 7ParisFrance
  4. 4.Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRSParisFrance
  5. 5.Laboratoire Léon BrillouinUMR12 CEA/CNRS, CEA—Centre de SaclayGif-sur-Yvette CedexFrance

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