A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
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DOI：
10.1093/bioinformatics/bth394
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发表时间：
2004-12-12
期刊：
影响因子：
5.8
通讯作者：
Furia, M
中科院分区：
文献类型：
--
作者：
Accardo, MC;Giordano, E;Furia, M
动机：在真核生物中，非编码 RNA 基因家族包括许多编码小核仁 RNA（主要是 C/D 和 H/ACA snoRNA）的基因，它们在靶 RNA 分子的成熟或转录后修饰中发挥指导作用。由于迄今为止，在果蝇 (Dm) 中，通过 cDNA 文库筛选仅鉴定了少数 snoRNA 实例，因此将分子数据与这些类型基因的计算机识别相结合，可以揭示它们在 Dm 基因组中的组织。 结果：我们对 Dm 基因组中的 C/D snoRNA 基因进行了计算筛选，然后对假定的候选基因进行了实验验证。 26 个已确认的 snoRNA 中很少有被 cDNA 文库分析所识别。还发现 Dm 基因组的组织比之前想象的更加多样化，snoRNA 基因嵌套在蛋白质编码基因的内含子和外显子中。这一发现表明，基于重叠 mRNA/snoRNA 分子的替代产生，存在额外的 snoRNA 生物发生机制。
Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome.Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules.