E-SGRP-8 - Transcription profiling of different developmental stages of Plasmodium falciparum to identify expression of non-coding RNAs

Status
Submitted on 13 November 2006, released on 23 August 2007, last updated on 2 May 2014
Organism
Plasmodium falciparum
Samples (9)
Array (1)
Protocols (7)
Description
In summary, we present a systematic in silico screen for the conserved non-coding RNA structures by comparing the P. falciparum genome with seven other malaria species and describe 668 candidate RNA secondary structures. By combining microarray and northern data, we provide evidence for expression of 28 novel ncRNA candidates at the transcript level in the blood stages of P. falciparum, a subset of which show intra-erythrocytic stage-specificity for expression. Few of the expressed novel candidates appear to have similarity to functionally known ncRNAs characterised to-date. The ncRNA candidates that show a narrow phylogenetic distribution, such as the internal var-associated ncRNAs, may be involved in species-specific function. At present, we can not assign specific function to these novel ncRNAs, however, our study highlights the abundance of these novel ncRNA structures in P. falciparum and suggests important roles for these ncRNAs in cellular processes. Although the control of gene expression by mechanisms such as epigenetics, post-transcriptional gene regulation and transcript stability has been recently shown in Plasmodium, all the key cellular players in such types of non-conventional gene regulation in Plasmodium are yet to be identified. Taking cues from the functionally characterized components of the higher eukaryotic non-coding RNA populations, it is tempting to speculate that ncRNAs may, at least in part, be instrumental in gene regulation in P. falciparum. However, in contrast to the higher eukaryotes, the absence of a conventional RNAi pathway and its associated components in malaria suggests that these malaria-specific novel ncRNAs, where functional, must exert their role using novel pathways or mechanisms, possibly unique to malaria. It remains to be determined what fraction of the ncRNAs described here are involved in modulating expression of one or more genes or gene families in malaria and also the precise cellular function for them not only in the blood stages but also in the other life-cycle stages of P. falciparum.
Experiment types
transcription profiling by array, co-expression, development or differentiation, replicate
Contact
Citation
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A. Genome Res 18(2):281-292 (2008), Europe PMC 18096748
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-SGRP-8.idf.txt
Sample and data relationshipE-SGRP-8.sdrf.txt
Raw data (1)E-SGRP-8.raw.1.zip
Processed data (1)E-SGRP-8.processed.1.zip
Array designA-AFFY-80.adf.txt
R ExpressionSetE-SGRP-8.eSet.r
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