Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs
<p>Abstract</p> <p>Background</p> <p>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. Chicken snoRNAs have been very poorly characterized when compa...
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| Format: | Article |
| Language: | English |
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BMC
2009-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/86 |
| _version_ | 1811316907523964928 |
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| author | Guan Dao-Gang Zhou Hui Yang Jian-Hua Shao Peng Qu Liang-Hu |
| author_facet | Guan Dao-Gang Zhou Hui Yang Jian-Hua Shao Peng Qu Liang-Hu |
| author_sort | Guan Dao-Gang |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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. 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.</p> <p>Results</p> <p>Two 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 <it>gas5</it>-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.</p> <p>Conclusion</p> <p>We 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.</p> |
| first_indexed | 2024-04-13T11:57:24Z |
| format | Article |
| id | doaj.art-c168d28414c342e4a821163736a94fd4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T11:57:24Z |
| publishDate | 2009-02-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-c168d28414c342e4a821163736a94fd42022-12-22T02:47:53ZengBMCBMC Genomics1471-21642009-02-011018610.1186/1471-2164-10-86Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAsGuan Dao-GangZhou HuiYang Jian-HuaShao PengQu Liang-Hu<p>Abstract</p> <p>Background</p> <p>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. 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.</p> <p>Results</p> <p>Two 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 <it>gas5</it>-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.</p> <p>Conclusion</p> <p>We 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.</p>http://www.biomedcentral.com/1471-2164/10/86 |
| spellingShingle | Guan Dao-Gang Zhou Hui Yang Jian-Hua Shao Peng Qu Liang-Hu Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs BMC Genomics |
| title | Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs |
| title_full | Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs |
| title_fullStr | Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs |
| title_full_unstemmed | Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs |
| title_short | Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs |
| title_sort | genome wide analysis of chicken snornas provides unique implications for the evolution of vertebrate snornas |
| url | http://www.biomedcentral.com/1471-2164/10/86 |
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