ArticleBMC genomics2009
Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 43 citations in OpenAlex.
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- The regulatory roles of small nucleolar RNAs within their host locus.RNA biology · 2024Review
- SnoRNA copy regulation affects family size, genomic location and family abundance levels.BMC genomics · 2021Article
- Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites.RNA (New York, N.Y.) · 2021Article
- "Lost and Found": snoRNA Annotation in the Xenopus Genome and Implications for Evolutionary Studies.Molecular biology and evolution · 2020Article
- The yeast noncoding RNA interaction network.RNA (New York, N.Y.) · 2017Article
- SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.BMC bioinformatics · 2016Article
- Phylogenetic distribution of plant snoRNA families.BMC genomics · 2016Article
- ncRNA orthologies in the vertebrate lineage.Database : the journal of biological databases and curation · 2016Article
- Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved.RNA (New York, N.Y.) · 2015Article
- Conservation and losses of non-coding RNAs in avian genomes.PloS one · 2015Article
- SNOntology: Myriads of novel snoRNAs or just a mirage?BMC genomics · 2011Article
- Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori.Nucleic acids research · 2011Article
- Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.PLoS biology · 2010Article
- Systematic identification and characterization of chicken (Gallus gallus) ncRNAs.Nucleic acids research · 2009Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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