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Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli

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Bacterial Regulatory RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1737))

Abstract

Regulation of RNA turnover is of utmost importance for controlling the concentration of transcripts and consequently cellular protein levels. Among the processes controlling RNA decay, small noncoding regulatory RNAs (sRNAs) have recently emerged as major new players. In this chapter, we describe and discuss protocols that can be used to measure sRNA concentration in vivo and to assess sRNA decay rates in Gram-negative bacteria. Precisely, we focus our analyses on the Escherichia coli Gram-negative bacterium as a model. The information described in this chapter provides a guideline to help develop a protocol in order to assess these important parameters and to identify RNA-processing enzymes involved in sRNA degradation processes.

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Abbreviations

ncRNA:

Noncoding RNA

nt:

Nucleotide

NTD/CTD:

N-terminal/C-terminal domain

PAGE:

PolyAcrylamide gel electrophoresis

PAP:

Poly(A) polymerase

PNPase:

Polynucleotide phosphorylase

RNAP:

RNA polymerase

RNAse:

Ribonuclease

sRNA:

Small RNA

ss/ds:

Single/double stranded

Tm :

Melting temperature

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Acknowledgments

This work was supported by the CNRS, CEA, and University Paris Diderot. We are particularly grateful to Bastien Cayrol (INRA/CIRAD) for his help in preparing this manuscript, and to Richard Lease (Ohio State Univ.) and Daniele Joseleau-Petit (Univ. Paris Diderot) for critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Université Paris Diderot & LLB/CEA/CNRS, Gif-sur-Yvette, France

    Florent Busi & Véronique Arluison

  2. Unité de Biologie Fonctionnelle et Adaptative, CNRS UMR 8251, Paris, France

    Florent Busi

  3. Laboratoire Expression Génétique Microbienne UMR8261 CNRS/Université Paris Diderot Institut de Biologie Physico-Chimique IBPC, Paris, France

    Philippe Régnier

Authors
  1. Florent Busi
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  2. Véronique Arluison
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  3. Philippe Régnier
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Corresponding author

Correspondence to Florent Busi .

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Editors and Affiliations

  1. Université Paris Diderot & LLB/CEA/CNRS, Gif-sur-Yvette, France

    Véronique Arluison

  2. Laboratorio de Bioquímica, Microbiología e Interacciones, Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Bernal, Argentina

    Claudio Valverde

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Busi, F., Arluison, V., Régnier, P. (2018). Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli . In: Arluison, V., Valverde, C. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 1737. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7634-8_14

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  • DOI: https://doi.org/10.1007/978-1-4939-7634-8_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7633-1

  • Online ISBN: 978-1-4939-7634-8

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