Noncoding RNA genes identified in AT-rich hyperthermophiles
Noncoding RNA genes identified in AT-rich hyperthermophiles
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DOI：
10.1073/pnas.112063799
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发表时间：
2002-05-28
影响因子：
11.1
通讯作者：
Eddy, SR
中科院分区：
文献类型：
--
作者：
Klein, RJ;Misulovin, Z;Eddy, SR
产生功能性 RNA 而不是编码蛋白质的非编码 RNA (ncRNA) 基因似乎比之前想象的更为普遍。然而，估计它们的数量和重要性很困难，因为系统鉴定 ncRNA 基因仍然具有挑战性。在这里，我们利用了一些超嗜热生物基因组中强烈的、令人惊讶的 DNA 组成偏差：简单地筛选富含 AT 的詹氏甲烷球菌和激烈火球菌基因组中富含 GC 的区域，即可有效检测具有高度二级结构的已知和新的 RNA 基因。基于比较分析的单独筛选也成功鉴定了 P. Furiosus 中的非编码 RNA 基因。这些筛选预测的 30 个新候选基因中有 9 个已被证实可产生离散的、明显非编码的转录本，其大小范围为 97 至 277 个核苷酸。
Noncoding RNA (ncRNA) genes that produce functional RNAs instead of encoding proteins seem to be somewhat more prevalent than previously thought. However, estimating their number and importance is difficult because systematic identification of ncRNA genes remains challenging. Here, we exploit a strong, surprising DNA composition bias in genomes of some hyperthermophilic organisms: simply screening for GC-rich regions in the AT-rich Methanococcus jannaschii and Pyrococcus furiosus genomes efficiently detects both known and new RNA genes with a high degree of secondary structure. A separate screen based on comparative analysis also successfully identifies noncoding RNA genes in P. furiosus. Nine of the 30 new candidate genes predicted by these screens have been verified to produce discrete, apparently noncoding transcripts with sizes ranging from 97 to 277 nucleotides.