Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae).
Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae).
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DOI：
10.1371/journal.pone.0019350
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发表时间：
2011-04-28
期刊：
影响因子：
3.7
通讯作者：
Belles X
中科院分区：
文献类型：
--
作者：
Cristino AS;Tanaka ED;Rubio M;Piulachs MD;Belles X
据报道，microRNA (miRNA) 是真核细胞转录后水平的关键调节因子。在昆虫中，大多数研究都集中在全变态动物上，而最近才鉴定出两种半变态动物（飞蝗和豌豆蚜）的 miRNA。因此，对进化基础半变态德国小蠊的 miRNA 的研究可能为 miRNA 的结构和功能进化提供有价值的见解。德国蟑螂 B. germanica 的小 RNA 文库是由最后一龄若虫的整个身体和成虫卵巢构建的。高通量 Solexa 测序分别对全身和卵巢进行了约 11 和 800 万次读取。生物信息分析鉴定出 38 种已知 miRNA 以及 11 种已知 miRNA*。我们还发现了 70 个在其他昆虫中保守的 miRNA 候选者和 170 个德国小蠹特有的候选者。 Solexa 数据与实时定量 PCR 之间的正相关性表明，reads 数可以作为定量方法。通过 PCR 和测序鉴定并验证了五种新的 miRNA 前体。已知的 miRNA 和新的候选物也通过在 dicer-1 RNAi 敲除个体中降低其表达水平进行了验证。两个文库的比较表明，若虫全身含有比卵巢更多的已知 miRNA，而成虫卵巢则富含新的 miRNA 候选物。我们的研究在基础半变态昆虫德国芽孢杆菌中鉴定出许多已知的miRNA和新的miRNA候选物，并且大多数特定序列在卵巢中发现。深度测序数据反映了 miRNA 丰度，dicer-1 RNAi 检测被证明是验证新型 miRNA 的可靠方法。
microRNAs (miRNAs) have been reported as key regulators at post-transcriptional level in eukaryotic cells. In insects, most of the studies have focused in holometabolans while only recently two hemimetabolans (Locusta migratoria and Acyrthosiphon pisum) have had their miRNAs identified. Therefore, the study of the miRNAs of the evolutionarily basal hemimetabolan Blattella germanica may provide valuable insights on the structural and functional evolution of miRNAs. Small RNA libraries of the cockroach B. germanica were built from the whole body of the last instar nymph, and the adult ovaries. The high throughput Solexa sequencing resulted in approximately 11 and 8 million reads for the whole-body and ovaries, respectively. Bioinformatic analyses identified 38 known miRNAs as well as 11 known miRNA*s. We also found 70 miRNA candidates conserved in other insects and 170 candidates specific to B. germanica. The positive correlation between Solexa data and real-time quantitative PCR showed that number of reads can be used as a quantitative approach. Five novel miRNA precursors were identified and validated by PCR and sequencing. Known miRNAs and novel candidates were also validated by decreasing levels of their expression in dicer-1 RNAi knockdown individuals. The comparison of the two libraries indicates that whole-body nymph contain more known miRNAs than ovaries, whereas the adult ovaries are enriched with novel miRNA candidates. Our study has identified many known miRNAs and novel miRNA candidates in the basal hemimetabolan insect B. germanica, and most of the specific sequences were found in ovaries. Deep sequencing data reflect miRNA abundance and dicer-1 RNAi assay is shown to be a reliable method for validation of novel miRNAs.
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DOI：
10.1073/pnas.0805943105
发表时间：
2008-09-30
影响因子：
11.1
作者：
Chambeyron, Severine;Popkova, Anna;Bucheton, Alain
通讯作者：
Bucheton, Alain
DOI：
10.1073/pnas.0907391106
发表时间：
2009-12-22
影响因子：
11.1
作者：
Gomez-Orte, Eva;Belles, Xavier
通讯作者：
Belles, Xavier
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun
DOI：
10.1073/pnas.0509535102
发表时间：
2005-12-27
影响因子：
11.1
作者：
Kwon, C;Han, Z;Srivastava, D
通讯作者：
Srivastava, D
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.