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A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants

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Part of the Methods in Molecular Biology book series (MIMB,volume 2494)

Abstract

Protein production from mRNA is one of the fundamental molecular processes in a cell. Accurate genome-wide information on the levels of translation and ribosome distribution on mRNA can be gathered by carrying out ribosome footprinting, aka Ribo-seq. Herein, we present a detailed protocol describing the construction of parallel Ribo-seq and RNA-seq libraries from Arabidopsis seedlings treated with the plant hormone auxin. The improved protocol for ribosome footprint library generation can be easily adapted to analyzing the effects on translation of genetic perturbations and various abiotic and biotic factors to shed the much-needed light on translational regulation in plants.

Key words

  • Ribo-seq
  • RNA-seq
  • Translation
  • Translational regulation
  • Arabidopsis

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  • DOI: 10.1007/978-1-0716-2297-1_6
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Acknowledgments

The research in the Alonso-Stepanova Laboratory is supported by the National Science Foundation grants 1650139, 1444561, and 1940829 to ANS and JMA and 1750006 to ANS. We are thankful to Dr. Mario Fenech for the critical reading of this manuscript.

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Correspondence to Anna N. Stepanova .

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Chen, H., Alonso, J.M., Stepanova, A.N. (2022). A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants. In: Duque, P., Szakonyi, D. (eds) Environmental Responses in Plants. Methods in Molecular Biology, vol 2494. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2297-1_6

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  • DOI: https://doi.org/10.1007/978-1-0716-2297-1_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2296-4

  • Online ISBN: 978-1-0716-2297-1

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