Genome Biology and Evolution Advance Access originally published online on November 5, 2009
Genome Biology and Evolution (2009) Vol. 2009:420; doi:10.1093/gbe/evp045 published on November 23, 2009
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Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes
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* Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
E-mail: anthony.poole{at}canterbury.ac.nz.
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Abstract |
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Small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) are integral to a range of processes, including ribosome biogenesis and gene regulation. Some are intron encoded, and this organization may facilitate coordinated coexpression of host gene and RNA. However, snoRNAs and miRNAs are known to be mobile, so intron-RNA associations may not be evolutionarily stable. We have used genome alignments across 11 mammals plus chicken to examine positional orthology of snoRNAs and miRNAs and report that 21% of annotated snoRNAs and 11% of miRNAs are positionally conserved across mammals. Among RNAs traceable to the bird–mammal common ancestor, 98% of snoRNAs and 76% of miRNAs are intronic. Comparison of the most evolutionarily stable mammalian intronic snoRNAs with those positionally conserved among primates reveals that the former are more overrepresented among host genes involved in translation or ribosome biogenesis and are more broadly and highly expressed. This stability is likely attributable to a requirement for overlap between host gene and intronic snoRNA expression profiles, consistent with an ancestral role in ribosome biogenesis. In contrast, whereas miRNA positional conservation is comparable to that observed for snoRNAs, intronic miRNAs show no obvious association with host genes of a particular functional category, and no statistically significant differences in host gene expression are found between those traceable to mammalian or primate ancestors. Our results indicate evolutionarily stable associations of numerous intronic snoRNAs and miRNAs and their host genes, with probable continued diversification of snoRNA function from an ancestral role in ribosome biogenesis.
Keywords: snoRNA, miRNA, intron, evolution
Accepted October 31, 2009