NcRNA-microchip analysis: a novel approach to identify differential expression of noncoding RNAs.
RNA Biol, 2010/9-2010/10;7(5):586-95.
Hutzinger R[1], Mrázek J, Vorwerk S, Hüttenhofer A
Affiliations
PMID: 21037422
Impact factor: 4.766
Abstract
Epstein-Barr virus (EBV) infection of human B cells requires the presence of non-coding RNAs (ncRNAs), which regulate expression of viral and host genes. To identify differentially expressed regulatory ncRNAs involved in EBV infection, a specialized cDNA library, enriched for ncRNAs derived from EBV-infected cells, was subjected to deep-sequencing. From the deep-sequencing analysis, we generated a custom-designed ncRNA-microchip to investigate differential expression of ncRNA candidates. By this approach, we identified 25 differentially expressed novel host-encoded ncRNA candidates in EBV-infected cells, comprised of six non-repeat-derived and 19 repeat-derived ncRNAs. Upon EBV infection of B cells, we also observed increased expression levels of oncogenic miRNAs mir-221 and mir-222, which might contribute to EBV-related tumorigenesis, as well as decreased expression levels of RNase P RNA, a ribozyme involved in tRNA maturation. Thus, in this study we demonstrate that our ncRNA-microchip approach serves as a powerful tool to identify novel differentially expressed ncRNAs acting as potential regulators of gene expression during EBV infection.
MeSH terms
B-Lymphocytes; Epstein-Barr Virus Infections; Gene Expression Profiling; Herpesvirus 4, Human; Humans; Microchip Analytical Procedures; RNA, Untranslated
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