Hubrecht Institute-KNAW & University Medical Center Utrecht, Cancer Genomics Center, Utrecht, The Netherlands.
BMC Genomics. 2010 Apr 19;11:249. doi: 10.1186/1471-2164-11-249.
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.
数字基因表达（DGE）分析已成为研究 RNA 表达的一种既定工具。在这里，我们对来自两个不同大鼠品系（BN-Lx 和 SHR）的六个不同大鼠组织（脾、肝、脑、睾丸、心、肾）的小 RNA DGE 图谱进行了深入分析。我们描述了已知和新的 micro（mi）RNA 和 piwi 相互作用（pi）RNA 的表达模式。
我们证实了 588 个已知 miRNA（54 个为反义方向）的表达，并鉴定出 56 个与已知人类或小鼠 miRNA 同源的 miRNA，以及 45 个新的大鼠 miRNA。此外，我们证实了脑内 mir-376a/b/c 的特定 A 到 I 编辑，并确定 mir-377 为新的编辑靶标。与早期的发现一致，我们观察到所有分析的组织都表现出高度的组织特异性表达模式。大脑被发现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肝脏中存在强烈的品系特异性差异 miRNA 表达，这是由两个品系之间的遗传变异引起的。最后，我们在睾丸中鉴定出两种类型的生殖系特异性 piRNA，分别映射到转座子或链特异性簇中。
总之，这里描述的小 RNA 总集推进了大鼠基因组中小 RNA 的注释。品系和组织特异性表达模式为研究小 RNA 在调控网络以及在该模型系统中广泛研究的生理和神经生物学等生物学过程中的作用提供了坚实的基础。
