School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
BMC Genomics. 2012 Aug 14;13:390. doi: 10.1186/1471-2164-13-390.
Small nucleolar RNAs are a highly conserved group of small RNAs found in eukaryotic cells. Genes encoding these RNAs are diversely located throughout the genome. They are functionally conserved, performing post transcriptional modification (methylation and pseudouridylation) of rRNA and other nuclear RNAs. They belong to two major categories: the C/D box and H/ACA box containing snoRNAs. U3 snoRNA is an exceptional member of C/D box snoRNAs and is involved in early processing of pre-rRNA. An antisense sequence is present in each snoRNA which guides the modification or processing of target RNA. However, some snoRNAs lack this sequence and often they are called orphan snoRNAs.
We have searched snoRNAs of Entamoeba histolytica from the genome sequence using computational programmes (snoscan and snoSeeker) and we obtained 99 snoRNAs (C/D and H/ACA box snoRNAs) along with 5 copies of Eh_U3 snoRNAs. These are located diversely in the genome, mostly in intergenic regions, while some are found in ORFs of protein coding genes, intron and UTRs. The computationally predicted snoRNAs were validated by RT-PCR and northern blotting. The expected sizes were in agreement with the observed sizes for all C/D box snoRNAs tested, while for some of the H/ACA box there was indication of processing to generate shorter products.
Our results showed the presence of snoRNAs in E. histolytica, an early branching eukaryote, and the structural features of E. histolytica snoRNAs were well conserved when compared with yeast and human snoRNAs. This study will help in understanding the evolution of these conserved RNAs in diverse phylogenetic groups.
小核仁 RNA 是真核细胞中高度保守的一组小 RNA。编码这些 RNA 的基因在基因组中广泛分布。它们在功能上是保守的，执行 rRNA 和其他核 RNA 的转录后修饰（甲基化和假尿嘧啶化）。它们属于两个主要类别：包含 snoRNA 的 C/D 盒和 H/ACA 盒。U3 snoRNA 是 C/D 盒 snoRNA 的一个特殊成员，参与 pre-rRNA 的早期加工。每个 snoRNA 都存在一个反义序列，该序列指导靶 RNA 的修饰或加工。然而，一些 snoRNA 缺乏此序列，通常被称为孤儿 snoRNA。
我们使用计算程序（snoscan 和 snoSeeker）从基因组序列中搜索了溶组织内阿米巴的 snoRNA，获得了 99 个 snoRNA（C/D 和 H/ACA 盒 snoRNA），以及 5 个 Eh_U3 snoRNA 拷贝。这些 snoRNA 广泛分布在基因组中，主要位于基因间区，而有些位于蛋白编码基因的 ORF、内含子和 UTR 中。通过 RT-PCR 和 northern blot 验证了计算预测的 snoRNA。所有测试的 C/D 盒 snoRNA 的预期大小与观察到的大小一致，而一些 H/ACA 盒 snoRNA 存在加工产生较短产物的迹象。
我们的结果表明，溶组织内阿米巴中存在 snoRNA，这是一种早期分支的真核生物，与酵母和人类 snoRNA 相比，溶组织内阿米巴 snoRNA 的结构特征得到了很好的保守。这项研究将有助于理解这些保守 RNA 在不同系统发育群中的进化。
