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

TY - JOUR

T1 - Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

AU - Mourier, Tobias

AU - Carret, Celine

AU - Kyes, Sue

AU - Christodoulou, Zoe

AU - Gardner, Paul P

AU - Jeffares, Daniel C

AU - Pinches, Robert

AU - Barrell, Bart

AU - Berriman, Matt

AU - Griffiths-Jones, Sam

AU - Ivens, Alasdair

AU - Newbold, Chris

AU - Pain, Arnab

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

U2 - 10.1101/gr.6836108

DO - 10.1101/gr.6836108

M3 - Journal article

C2 - 18096748

SN - 1088-9051

VL - 18

SP - 281

EP - 292

JO - Genome Research

JF - Genome Research

IS - 2

ER -