MBE Advance Access published online on April 29, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm084
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© 2007 The Authors.
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-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Research Article |
The Ro Associated Y RNAs in Metazoans: Evolution and Diversification
1 Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke (Québec), J1H 5N4, Canada
2 Service de rhumatologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke (Québec), J1H 5N4, Canada
* Corresponding authors: Gilles Boire M.D., M.Sc., Professor and Rheumatologist, Email : Gilles.Boire{at}USherbrooke.ca, Phone : (819) 564-5261; Fax : (819) 564-5265, Jean-Pierre Perreault Ph.D, Professor, Email: Jean-Pierre.Perreault{at}USherbrooke.ca, Phone : (819) 564-5310; Fax : (819) 564-5340
Received for publication February 13, 2007. Revision received April 16, 2007. Accepted for publication April 20, 2007.
The Y genes encode small non-coding RNAs whose functions remain elusive, whose numbers vary between species, and whose major property is to be bound by the Ro60 protein (or its ortholog in other species). To better understand the evolution of the Y gene family, we performed a homology search in 27 different genomes along with a structural search using Y RNA specific motifs. These searches confirmed that Y RNAs are well conserved in the animal kingdom and resulted in the detection of several new Y RNA genes, including the first Y RNAs in insects and a second Y RNA detected in Caenorhabditis elegans. Unexpectedly, Y5 genes were retrieved almost as frequently as Y1 and Y3 genes, and, consequently are not the result of a relatively recent apparition as is generally believed. Investigation of the organization of the Y genes demonstrated that the synteny was conserved among species. Interestingly, it revealed the presence of six putative "fossil" Y genes, all of which were Y4 and Y5 related. Sequence analysis led to inference of the ancestral sequences for all Y RNAs. In addition, the evolution of existing Y RNAs was deduced for many families, orders and classes. Moreover, a consensus sequence and secondary structure for each Y species was determined. Further evolutionary insight was obtained from the analysis of several thousand Y retropseudogenes among various species. Taken together, these results confirm the rich and diversified evolution history of Y RNAs.
Key Words: Y RNA • retroposition • retrotransposition • pseudogene • ancestral genes
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