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Nucleic Acids Research 2006 34(2):635-646; doi:10.1093/nar/gkj469
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Published online 25 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

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Experimental approaches to identify non-coding RNAs

Alexander Hüttenhofer* and Jörg Vogel1

Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria 1Max Planck Institute for Infection Biology Schumannstrasse 21-22, 10117 Berlin, Germany

*To whom correspondence should be addressed. Tel: +43 (0) 512 507 3630; Fax: +43 (0) 512 507 9880; Email: alexander.huettenhofer{at}i-med.ac.at

Received December 21, 2005. Revised January 10, 2006. Accepted January 10, 2006.

Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.


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