Published online 31 May 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray
1 Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, China 2 Computational Biology Research Group, Division of Intelligent Software Systems, Institute of Computing Technology, Chinese Academy of Sciences Beijing 100080, China 3 Chinese National Human Genome Center Beijing 100176, China 4 Department of Molecular Sciences/Center of Genomics and Bioinformatics, University of Tennessee Health Science Center Memphis, TN 38163, USA 5 Graduate School of the Chinese Academy of Sciences Beijing 100080, China 6 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Beijing, China 7 Beijing Genomics Institute, Chinese Academy of Sciences Beijing 101300, China
*To whom correspondence should be addressed at Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Tel: +86 10 64888543; Fax: +86 10 64889892; Email: crs{at}sun5.ibp.ac.cn
Received January 17, 2006. Revised March 8, 2006. Accepted April 27, 2006.
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA–host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of ‘expressional freedom’, depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism.
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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