Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

  1. Tobias Mourier1,2,7,
  2. Celine Carret3,7,
  3. Sue Kyes4,7,
  4. Zoe Christodoulou4,
  5. Paul P. Gardner5,
  6. Daniel C. Jeffares3,
  7. Robert Pinches4,
  8. Bart Barrell3,
  9. Matt Berriman3,
  10. Sam Griffiths-Jones6,
  11. Alasdair Ivens3,
  12. Chris Newbold4, and
  13. Arnab Pain3,8
  1. 1 Ancient DNA and Evolution Group, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark;
  2. 2 Department of Experimental Medical Science, Lund University, Lund 22184, Sweden;
  3. 3 Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom;
  4. 4 Molecular Parasitology Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom;
  5. 5 Department of Molecular Biology, University of Copenhagen, Copenhagen DK-2200, Denmark;
  6. 6 Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom

  1. ↵7 These authors contributed equally to this work.

Abstract

We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured ncRNAs in P. falciparum and are not represented in any RNA databases. We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism’s life cycle.

Footnotes

  • ↵8 Corresponding author.

    ↵8 E-mail ap2{at}sanger.ac.uk; fax 44-01223-494919.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6836108

    • Received June 23, 2007.
    • Accepted October 23, 2007.

  • Freely available online through the Genome Research Open Access option.

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  1. Published in Advance December 20, 2007, doi: 10.1101/gr.6836108 Genome Res. 18: 281-292 Copyright © 2008, Cold Spring Harbor Laboratory Press

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