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Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation

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Pseudogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1167))

Abstract

Pseudogenes may regulate expression of their parental genes as well as other protein-coding genes through various mechanisms. One such mechanism is the ability to act as competitive endogenous RNA (ceRNA) and participate in microRNA-mediated cross-regulation. Here, we outline how to predict the targets of pseudogene ceRNAs bioinformatically and how to validate them experimentally.

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Acknowledgments

We thank members of the Pandolfi lab for critical reading of the manuscript. F.A.K. was supported by a Department of Defense Prostate Cancer Research Program fellowship. P.P. and U.A. received support from AIRC under grant IG-9408, and P.P.P. from NCI (R01 CA170158).

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Authors and Affiliations

  1. Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, CLS-401, Boston, MA, 02215, USA

    Florian A. Karreth & Pier Paolo Pandolfi M.D., Ph.D.

  2. Molecular Biotechnology Center and Department of Biotechnology and Life Sciences, University of Turin, Turin, Italy

    Ugo Ala & Paolo Provero

  3. Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy

    Paolo Provero

Authors
  1. Florian A. Karreth
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  2. Ugo Ala
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  3. Paolo Provero
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  4. Pier Paolo Pandolfi M.D., Ph.D.
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Corresponding author

Correspondence to Pier Paolo Pandolfi M.D., Ph.D. .

Editor information

Editors and Affiliations

  1. Istituto Toscano Tumori, Pisa, Italy

    Laura Poliseno

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© 2014 Springer Science+Business Media New York

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Karreth, F.A., Ala, U., Provero, P., Pandolfi, P.P. (2014). Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation. In: Poliseno, L. (eds) Pseudogenes. Methods in Molecular Biology, vol 1167. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0835-6_13

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  • DOI: https://doi.org/10.1007/978-1-4939-0835-6_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0834-9

  • Online ISBN: 978-1-4939-0835-6

  • eBook Packages: Springer Protocols

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