Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation.
Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation.
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DOI：
10.1371/journal.pone.0034394
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Chen T
中科院分区：
文献类型：
--
作者：
Meng F;Hackenberg M;Li Z;Yan J;Chen T
microRNAs（miRNAs）是一类小的非编码RNA，参与调节多种生物学过程。最新版本的miRBase数据库（Release 18）包括1，157个小鼠和680个大鼠成熟miRNAs。在miRBase第16版至第18版的大鼠miRNA数据库中，仅添加了一个新的大鼠成熟miRNA，这表明仍有许多大鼠miRNA有待发现。鉴于大鼠作为模式生物的重要性，发现完整的大鼠miRNA对于理解大鼠miRNA调控是必要的。本研究应用新一代测序技术、微阵列分析技术和生物信息学技术，对大鼠肾脏中的miRNAs进行了研究。利用MiRanalyzer分析从大鼠肾脏样品的NGS分析产生的小RNA的序列。数百种新的miRNA候选者根据其读段到大鼠基因组的映射、可以在映射位置周围形成miRNA发夹结构的序列的存在、Dicer切割模式以及通过NGS和微阵列分析确定的其表达水平进行了检查。9个新的大鼠发夹前体miRNA（pre-miRNA）被发现具有高的置信度。在其他物种中也报道了五种新的pre-miRNAs，其中四种是大鼠特异性的。综上所述，通过NGS、微阵列和生物信息学高通量技术的组合，鉴定了9种新的pre-miRNAs（14种新的成熟miRNAs）。
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. The latest version of the miRBase database (Release 18) includes 1,157 mouse and 680 rat mature miRNAs. Only one new rat mature miRNA was added to the rat miRNA database from version 16 to version 18 of miRBase, suggesting that many rat miRNAs remain to be discovered. Given the importance of rat as a model organism, discovery of the completed set of rat miRNAs is necessary for understanding rat miRNA regulation. In this study, next generation sequencing (NGS), microarray analysis and bioinformatics technologies were applied to discover novel miRNAs in rat kidneys. MiRanalyzer was utilized to analyze the sequences of the small RNAs generated from NGS analysis of rat kidney samples. Hundreds of novel miRNA candidates were examined according to the mappings of their reads to the rat genome, presence of sequences that can form a miRNA hairpin structure around the mapped locations, Dicer cleavage patterns, and the levels of their expression determined by both NGS and microarray analyses. Nine novel rat hairpin precursor miRNAs (pre-miRNA) were discovered with high confidence. Five of the novel pre-miRNAs are also reported in other species while four of them are rat specific. In summary, 9 novel pre-miRNAs (14 novel mature miRNAs) were identified via combination of NGS, microarray and bioinformatics high-throughput technologies.
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影响因子：
56.9
作者：
Lagos-Quintana, M;Rauhut, R;Tuschl, T
通讯作者：
Tuschl, T
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
12.3
作者：
Hendrix D;Levine M;Shi W
通讯作者：
Shi W
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
DOI：
10.1504/ijbra.2009.028678
发表时间：
2009-01-01
影响因子：
--
作者：
Gomase, Virendra S;Parundekar, Akshay N
通讯作者：
Parundekar, Akshay N