Corcoran David L, Pandit Kusum V, Gordon Ben, Bhattacharjee Arindam, Kaminski Naftali, Benos Panayiotis V
Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
PLoS One. 2009;4(4):e5279. doi: 10.1371/journal.pone.0005279. Epub 2009 Apr 23.
MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown.
We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters.
miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex.
微小RNA(miRNA)是蛋白质编码基因的短链非编码RNA调节因子。miRNA在多种生物学过程和各种疾病中发挥着非常重要的作用。许多算法能够预测miRNA基因及其靶标,但其转录调控仍在研究中。一般认为,基因内miRNA(位于蛋白质编码基因的内含子或外显子中)与其宿主基因共同转录,大多数基因间miRNA由其自身的RNA聚合酶II(Pol II)启动子转录。然而,初级转录本的长度和启动子组织目前尚不清楚。
我们使用围绕已知miRNA基因区域的定制芯片进行了Pol II染色质免疫沉淀(ChIP)-芯片实验。为了确定miRNA基因真正的核心转录起始位点,我们开发了一种新工具(CPPP)。我们发现miRNA基因可以从数千碱基外的启动子转录,并且它们的启动子与蛋白质编码基因的启动子具有相同的一般特征。最后,我们发现证据表明多达26%的基因内miRNA可能从其自身独特的启动子转录。
miRNA启动子与蛋白质编码基因的启动子具有相似的特征,但miRNA转录本组织更为复杂。