Small RNA expression and strain specificity in the rat.
Small RNA expression and strain specificity in the rat.
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DOI：
10.1186/1471-2164-11-249
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发表时间：
2010-04-19
期刊：
影响因子：
4.4
通讯作者：
Cuppen E
中科院分区：
文献类型：
--
作者：
Linsen SE;de Wit E;de Bruijn E;Cuppen E
数字基因表达（DGE）分析已成为研究RNA表达的既定工具。在这里，我们提供了一个深入分析的小RNA DGE配置文件从两个不同的大鼠品系（BN-Lx和SHR）从六个不同的大鼠组织（脾，肝，脑，睾丸，心脏，肾）。我们描述了已知的和新的微（mi）RNA和piwi相互作用（pi）RNA的表达模式。我们证实了588个已知的miRNAs的表达（54个反义方向），并鉴定了56个与已知的人类或小鼠miRNAs同源的miRNAs，以及45个新的大鼠miRNAs。此外，我们证实了mir-376 a/B/c在脑中的特异性A至I编辑，并将mir-377鉴定为新的编辑靶标。根据早期的研究结果，我们观察到一个高度组织特异性的表达模式的所有组织分析。发现大脑表达最多的组织特异性miRNA，其次是睾丸。值得注意的是，我们的实验还揭示了由菌株之间的遗传变异引起的肝脏中的强菌株特异性差异miRNA表达。最后，我们在睾丸中鉴定了两种类型的生殖系特异性piRNA，映射到转座子或链特异性簇中。总之，这里描述的小RNA纲要推进了大鼠基因组中小RNA的注释。此外，菌株和组织特异性表达模式为研究小RNA在调控网络中的作用以及在该模型系统中广泛研究的生理学和神经生物学等生物过程提供了强有力的基础。
Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
7
作者：
de Wit, Elzo;Linsen, Sam E. V.;Berezikov, Eugene
通讯作者：
Berezikov, Eugene
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.
影响因子：
14.9
作者：
Kawahara, Yukio;Megraw, Molly;Kreider, Edward;Iizasa, Hisashi;Valente, Louis;Hatzigeorgiou, Artemis G.;Nishikura, Kazuko
通讯作者：
Nishikura, Kazuko
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y