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Genome-Wide Analysis of RNA–Protein Interactions in Plasmodium falciparum Using eCLIP-Seq

Part of the Methods in Molecular Biology book series (MIMB,volume 2369)

Abstract

Over the last decades, identification of RNA–proteins complexes and their binding sites was challenging. Recently, techniques based on crosslinking, immunoprecipitation, and high-throughput sequencing have been developed. An optimized method, called eCLIP-seq, enables to identify precisely the targeted RNAs as well as the transcriptome-wide binding sites at nucleotide resolution. Here we describe the eCLIP-seq protocol in asexual stages of the human malaria parasite, Plasmodium falciparum. This method could facilitate the characterization of RNA-binding proteins in this organism for which few data are currently available.

Key words

  • Plasmodium falciparum
  • eCLIP-seq
  • RNA-binding protein
  • RNA–protein complex

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Acknowledgments

This work was supported by the National Institutes of Allergy and Infectious Diseases of the National Institutes of Health (grant R01 AI142743 to K.L.R) and the University of California, Riverside (NIFA-Hatch-225935 to K.L.R).

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Correspondence to Karine G. Le Roch .

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Hollin, T., Abel, S., Le Roch, K.G. (2021). Genome-Wide Analysis of RNA–Protein Interactions in Plasmodium falciparum Using eCLIP-Seq. In: de Pablos, L.M., Sotillo, J. (eds) Parasite Genomics. Methods in Molecular Biology, vol 2369. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1681-9_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1681-9_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1680-2

  • Online ISBN: 978-1-0716-1681-9

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