Analysis of mRNA Abundance and Stability by Ribonuclease Protection Assay

  • Cristina Romero-López
  • Alicia Barroso-delJesus
  • Pablo MenendezEmail author
  • Alfredo Berzal-Herranz
Part of the Methods in Molecular Biology book series (MIMB, volume 809)


Gene expression is a multi-step process, which proceeds from DNA through RNA to protein. The tight regulation of this process is essential for overall cellular integrity and physiological homeostasis. Regulation of the messenger RNA (mRNA) levels has emerged as a crucial event in the modulation of the expression of genetic information. The mechanisms by which this process occurs have been extensively studied and begin to be much better understood. They involve a network of complex pathways that use intrinsic features of the target mRNA, like stability, to control its relative abundance in the cytoplasm. Thus, the analysis of the mRNA stability and abundance is essential to properly undertake gene expression studies. This chapter describes the ribonuclease protection assay, a widely accepted approach to evaluate the quality and amount of a target mRNA. This technique displays a higher sensitivity than classical Northern blot analysis and may be used either individually or in combination with other quantitative methods, such as quantitative reverse-transcription PCR, as complementary procedures rendering more complete and reliable information on gene expression.

Key words

RNA stability Ribonuclease protection assay Gene expression analysis RNA quality RNA abundance 



A.B.-H’s group is funded by grant BFU2009-08137 from the Spanish Ministry of Science and Innovation, grant CTS-5077 from the Junta de Andalucía, and by FEDER funds from the EU. P.M.’s group is supported by the Andalusian Health Department, Andalusian Innovation and Science Department (P08-CTS-3678 to P.M), the FIS (PI070026), the MICINN (PLE-2009-0111), and the Marie Curie (PIIF-GA-2009-236430). We are indebted to Dr. Saumitra Das for his kind gift of Fig. 2.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Cristina Romero-López
    • 1
  • Alicia Barroso-delJesus
    • 2
  • Pablo Menendez
    • 3
    Email author
  • Alfredo Berzal-Herranz
    • 1
  1. 1.Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la SaludGranadaSpain
  2. 2.Genomics Facility, Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la SaludGranadaSpain
  3. 3.Stem Cells, Development & Cancer Laboratory GENyO: Centre for Genomics and Oncology Pfizer-University of Granada-Andalusian Govermment, Parque Tecnológico de Ciencias de la IlustraciónGranadaSpain

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