Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.
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.
Mourier
Tobias
T
Ancient DNA and Evolution Group, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.
Carret
Celine
C
Kyes
Sue
S
Christodoulou
Zoe
Z
Gardner
Paul P
PP
Jeffares
Daniel C
DC
Pinches
Robert
R
Barrell
Bart
B
Berriman
Matt
M
Griffiths-Jones
Sam
S
Ivens
Alasdair
A
Newbold
Chris
C
Pain
Arnab
A
D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D015152:Blotting, Northern; D002874:Chromosome Mapping; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D018503:Genome, Protozoan / Q000235:genetics*; D046228:Microarray Analysis; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D010963:Plasmodium falciparum / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D022661:RNA, Untranslated