Abstract
BackgroundSmall nucleolar RNAs (snoRNAs) represent one of the largest groups of functionally diverse trans-acting non-protein-coding (npc) RNAs currently known in eukaryotic cells. Chicken snoRNAs have been very poorly characterized when compared to other vertebrate snoRNAs. A genome-wide analysis of chicken snoRNAs is therefore of great importance to further understand the functional evolution of snoRNAs in vertebrates.ResultsTwo hundred and one gene variants encoding 93 box C/D and 62 box H/ACA snoRNAs were identified in the chicken genome and are predicted to guide 86 2'-O-ribose methylations and 69 pseudouridylations of rRNAs and spliceosomal RNAs. Forty-four snoRNA clusters were grouped into four categories based on synteny characteristics of the clustered snoRNAs between chicken and human. Comparative analyses of chicken snoRNAs revealed extensive recombination and separation of guiding function, with cooperative evolution between the guiding duplexes and modification sites. The gas5-like snoRNA host gene appears to be a hotspot of snoRNA gene expansion in vertebrates. Our results suggest that the chicken is a good model for the prediction of functional snoRNAs, and that intragenic duplication and divergence might be the major driving forces responsible for expansion of novel snoRNA genes in the chicken genome.ConclusionWe have provided a detailed catalog of chicken snoRNAs that aids in understanding snoRNA gene repertoire differences between avians and other vertebrates. Our genome-wide analysis of chicken snoRNAs improves annotation of the 'darkness matter' in the npcRNA world and provides a unique perspective into snoRNA evolution in vertebrates.
Highlights
Small nucleolar RNAs represent one of the largest groups of functionally diverse trans-acting non-protein-coding RNAs currently known in eukaryotic cells
We provide for the first time a detailed catalog of chicken Small nucleolar RNAs (snoRNAs) that facilitates understanding of snoRNA gene repertoire differences between the avian and other vertebrate lineages
132 gene variants encoding 83 box C/D snoRNAs with the ability to guide 2'-O-ribose methylation at 86 residues in rRNAs and spliceosomal nuclear RNA (snRNA) and 10 orphan box C/D snoRNAs were identified from the G.gallus genome (Table 1, see Additional file 1 and 2)
Summary
Small nucleolar RNAs (snoRNAs) represent one of the largest groups of functionally diverse trans-acting non-protein-coding (npc) RNAs currently known in eukaryotic cells. The term small nucleolar RNAs (snoRNAs) was originally coined to describe the nucleolar localization of this group of RNAs relative to the other small nucleoplasmic RNAs. In sharp contrast to the relatively low abundance spliceosomal nuclear RNA (snRNA) species, snoRNAs represent one of the largest groups of functionally diverse trans-acting non-protein-coding RNAs (npcRNAs) currently known in eukaryotic cells [1,2]. Box H/ACA snoRNAs exhibit a common hairpin-hinge-hairpin-tail secondary structure with the H box (ANANNA, where N stands for any nucleotide) in the hinge region and the ACA motif three nucleotides from the 3' end of the molecule. During the post-transcriptional processing of diverse RNAs most members of the known C/D and H/ACA snoRNAs respectively guide 2'-Oribose methylation and pseudouridylation (Ψ). Many of them exhibit a tissuespecific or restricted expression pattern [6,7] and are linked to genomic imprinting [6]
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