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

Mourier, Tobias LU ; Carret, Celine; Kyes, Sue; Christodoulou, Zoe; Gardner, Paul P.; Jeffares, Daniel C.; Pinches, Robert; Barrell, Bart; Berriman, Matt and Griffiths-Jones, Sam, et al. (2008) In Genome Research 18(2). p.281-292
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... (More)
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. (Less)
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publication status
published
subject
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Genome Research
volume
18
issue
2
pages
281 - 292
publisher
Cold Spring Harbor Laboratory Press
external identifiers
  • wos:000252860700011
  • scopus:39049155568
ISSN
1549-5469
DOI
10.1101/gr.6836108
language
English
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yes
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bf9f7882-c1cc-45b8-92ab-79ad43666cf4 (old id 1198705)
date added to LUP
2008-09-10 16:24:36
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2017-11-19 03:55:10
@article{bf9f7882-c1cc-45b8-92ab-79ad43666cf4,
  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.},
  author       = {Mourier, Tobias and Carret, Celine and Kyes, Sue and Christodoulou, Zoe and Gardner, Paul P. and Jeffares, Daniel C. and Pinches, Robert and Barrell, Bart and Berriman, Matt and Griffiths-Jones, Sam and Ivens, Alasdair and Newbold, Chris and Pain, Arnab},
  issn         = {1549-5469},
  language     = {eng},
  number       = {2},
  pages        = {281--292},
  publisher    = {Cold Spring Harbor Laboratory Press},
  series       = {Genome Research},
  title        = {Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum},
  url          = {http://dx.doi.org/10.1101/gr.6836108},
  volume       = {18},
  year         = {2008},
}