| RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. | |
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MedLine Citation:
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PMID: 20150415 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Up to 450,000 non-coding RNAs (ncRNAs) have been predicted to be transcribed from the human genome. However, it still has to be elucidated which of these transcripts represent functional ncRNAs. Since all functional ncRNAs in Eukarya form ribonucleo-protein particles (RNPs), we generated specialized cDNA libraries from size-fractionated RNPs and validated the presence of selected ncRNAs within RNPs by glycerol gradient centrifugation. As a proof of concept, we applied the RNP method to human Hela cells or total mouse brain, and subjected cDNA libraries, generated from the two model systems, to deep-sequencing. Bioinformatical analysis of cDNA sequences revealed several hundred ncRNP candidates. Thereby, ncRNAs candidates were mainly located in intergenic as well as intronic regions of the genome, with a significant overrepresentation of intron-derived ncRNA sequences. Additionally, a number of ncRNAs mapped to repetitive sequences. Thus, our RNP approach provides an efficient way to identify new functional small ncRNA candidates, involved in RNP formation. |
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Authors:
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Mathieu Rederstorff; Stephan H Bernhart; Andrea Tanzer; Marek Zywicki; Katrin Perfler; Melanie Lukasser; Ivo L Hofacker; Alexander Hüttenhofer |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-02-11 |
Journal Detail:
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Title: Nucleic acids research Volume: 38 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2010 Jun |
Date Detail:
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Created Date: 2010-06-03 Completed Date: 2010-06-22 Revised Date: 2010-09-28 |
Medline Journal Info:
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Nlm Unique ID: 0411011 Medline TA: Nucleic Acids Res Country: England |
Other Details:
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Languages: eng Pagination: e113 Citation Subset: IM |
Affiliation:
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Division of Genomics and RNomics, Innsbruck Biocentre, Innsbruck Medical University, Innsbruck and Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Animals Base Sequence Brain Chemistry Conserved Sequence Exons Gene Expression Profiling Gene Library* Hela Cells Humans Introns Mice RNA, Untranslated / classification, isolation & purification, metabolism* Repetitive Sequences, Nucleic Acid Ribonucleoproteins / chemistry*, isolation & purification |
| Chemical | |
Reg. No./Substance:
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0/RNA, Untranslated; 0/Ribonucleoproteins |
| Comments/Corrections | |
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