Unknown,Transcriptomics,Genomics,Proteomics

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Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum

ABSTRACT: Intermediate-size noncoding RNAs (is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Plasmodium falciparum, which is the most virulent malaria parasite infecting human being. By using Illumina/Solexa paired-end sequencing of an is-ncRNA-specific library, we performed a systematic identification of novel is-ncRNAs in intraerythrocytic P. falciparum, strain 3D7. A total of 1,198 novel is-ncRNA candidates, including antisense, intergenic, and intronic is-ncRNAs, were identified. Bioinformatics analyses showed that the intergenic is-ncRNAs were the least conserved among different Plasmodium species, and antisense is-ncRNAs were more conserved than their sense counterparts. Twenty-two novel snoRNAs were identified, and eight potential novel classes of P. falciparum is-ncRNAs were revealed by clustering analysis. The expression of randomly selected novel is-ncRNAs was confirmed by RT-PCR and northern blotting assays. An obvious different expressional profile of the novel is-ncRNA between the early and late intraerythrocytic developmental stages of the parasite was observed. The expression levels of the antisense RNAs correlated with those of their cis-encoded sense RNA counterparts, suggesting that these is-ncRNAs are involved in the regulation of gene expression of the parasite. In conclusion, we accomplished a deep profiling analysis of novel is-ncRNAs in P. falciparum, analysed the conservation and structural features of these novel is-ncRNAs, and revealed their differential expression patterns during the development of the parasite. These findings provide important information. One RNA sample (50-500 nt ) from the mixed intraerythrocytic stage of P. falciparum 3D7, subjected to Illumina/Solexa paired-end sequencing

ORGANISM(S): Plasmodium falciparum

SUBMITTER: Chunyan Wei

PROVIDER: E-GEOD-45172 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project 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.

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Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum

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