Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters
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作者:
Chen, Chun-Long
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Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Univ Paris 11, F-91405 Orsay, France
CNRS, UMR 8080, F-91405 Orsay, FranceZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Chen, Chun-Long
[1
,2
,3
]
Chen, Chong-Jian
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Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Univ Paris 11, F-91405 Orsay, France
CNRS, UMR 8621, F-91405 Orsay, FranceZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Chen, Chong-Jian
[1
,2
,4
]
Vallon, Olivier
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Univ Paris 06, CNRS, UMR 7141, Inst Biol Physicochim, F-75005 Paris, FranceZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Vallon, Olivier
[5
]
Huang, Zhan-Peng
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Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R ChinaZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Huang, Zhan-Peng
[1
]
Zhou, Hui
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Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R ChinaZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Zhou, Hui
[1
]
Qu, Liang-Hu
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Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R ChinaZhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
Qu, Liang-Hu
[1
]
机构:
[1] Zhongshan Univ, Biotechnol Res Ctr, Minist Educ, State Key Lab Biocontrol,Key Lab Gene Engn, Guangzhou 510275, Guangdong, Peoples R China
[2] Univ Paris 11, F-91405 Orsay, France
[3] CNRS, UMR 8080, F-91405 Orsay, France
[4] CNRS, UMR 8621, F-91405 Orsay, France
[5] Univ Paris 06, CNRS, UMR 7141, Inst Biol Physicochim, F-75005 Paris, France
Chlamydomonas reinhardtii is a unicellular green alga, the lineage of which diverged from that of land plants >1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 box H/ACA families can potentially guide pseudouridylation at 62 sites. Remarkably, 242 of the snoRNA genes are arranged into 76 clusters, of which 77% consist of homologous genes produced by small local tandem duplications. At least 70 snoRNA gene clusters are found within introns of protein-coding genes. Although not exhaustive, this analysis reveals that C. reinhardtii has the highest number of intronic snoRNA gene clusters among eukaryotes. The prevalence of intronic snoRNA gene clusters in C. reinhardtii is similar to that of rice but in contrast with the one-snoRNA-per-intron organization of vertebrates and fungi and with that of Arabidopsis thaliana in which only a few intronic snoRNA gene clusters were identified. This analysis of C. reinhardtii snoRNA gene organization shows the functional importance of introns in a single-called organism and provides evolutionary insight into the origin of intron-encoded RNAs in the plant lineage.