Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters
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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DOI：
10.1534/genetics.107.086025
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发表时间：
2008-05-01
期刊：
影响因子：
3.3
通讯作者：
Qu, Liang-Hu
中科院分区：
文献类型：
--
作者：
Chen, Chun-Long;Chen, Chong-Jian;Qu, Liang-Hu
莱茵衣藻是一种单细胞绿藻，其谱系在超过 10 亿年前就与陆地植物的谱系不同。使用强大的小核仁 RNA (snoRNA) 挖掘平台筛选莱茵衣藻基因组，我们鉴定了 322 个 snoRNA 基因，分为 118 个家族。 74 个盒 C/D 家族可以潜在地指导核糖体 RNA (rRNA) 和 snRNA 96 个位点的甲基化，44 个盒 H/ACA 家族可以潜在地指导 62 个位点的假尿苷化。值得注意的是，242 个 snoRNA 基因排列成 76 个簇，其中 77% 由小型局部串联重复产生的同源基因组成。蛋白质编码基因的内含子内至少发现了 70 个 snoRNA 基因簇。尽管并不详尽，但该分析表明莱茵衣藻拥有真核生物中数量最多的内含子 snoRNA 基因簇。莱茵衣藻中内含子 snoRNA 基因簇的流行率与水稻相似，但与脊椎动物和真菌中每个内含子一个 snoRNA 的组织方式以及拟南芥中仅鉴定出少量内含子 snoRNA 基因簇的情况相反。对莱茵衣藻 snoRNA 基因组织的分析显示了内含子在单一生物体中的功能重要性，并提供了植物谱系中内含子编码 RNA 起源的进化见解。
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.