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Custom microchip analysis identifies differentially expressed non-coding RNAs in Epstein-Barr virus-infected B cells

ABSTRACT: Upon Epstein-Barr virus (EBV) infection of human B lymphocytes non-coding RNAs (ncRNAs) regulate expression of viral and cellular genes. In this study, we generated a specialized cDNA library from EBV-immortalized cells and subjected it to deep sequencing. We identified 631 unique ncRNA genes, comprised of 321 potential novel differentially expressed ncRNA candidates. Subsequently, we investigated differential expression of known and potential novel ncRNA candidates by custom-designed microchips by comparing expression of ncRNA genes of EBV-immortalized versus non-infected control cells. Among the differentially expressed candidates from chip analysis, differential expression of six novel ncRNA candidates was verified by northern blot analysis. In addition, microchip analysis resulted in observation of increased expression levels of a significant number of potential ncRNA candidates that were preferentially derived from genomic loci annotated as Alu repetitive elements. Alu elements are members of the repeat subfamily of short interspersed nuclear elements (SINE) and were reported to be transcribed upon stress stimulation. While EBV infection significantly up-regulated expression of Alu-derived RNA transcripts, no significant increase in expression of these transcripts was observed under additional tested stress conditions. By employing deep sequencing followed by custom microchip analysis, we identified six novel differentially expressed ncRNAs as well as significantly increased expression levels of Alu-derived RNA transcripts. These transcripts might be involved in crucial functions upon infection by EBV.

ORGANISM(S): Homo sapiens Human herpesvirus 4 strain B95-8

PROVIDER: GSE20441 | GEO | 2010/10/30

SECONDARY ACCESSION(S): PRJNA125029

REPOSITORIES: GEO

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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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Custom microchip analysis identifies differentially expressed non-coding RNAs in Epstein-Barr virus-infected B cells

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