Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.
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转录，转录后和染色质相关的PRI-MIRNA，前MIRNA和MORNA的调节。
DOI：
10.1093/nar/gkv1354
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发表时间：
2016-04-20
影响因子：
14.9
通讯作者：
Lenhard B
中科院分区：
文献类型：
--
作者：
Nepal C;Coolen M;Hadzhiev Y;Cussigh D;Mydel P;Steen VM;Carninci P;Andersen JB;Bally-Cuif L;Müller F;Lenhard B
microRNA（miRNAs）在靶基因的转录后调控中发挥重要作用，尤其是在发育和分化过程中。我们对miRNA基因转录调控的理解受到初级miRNA（pri-miRNA）转录本注释不足的限制。在这里，我们使用CAGE-seq和RNA-seq来提供全基因组范围内的pri-miRNA核心启动子库及其在斑马鱼胚胎发生过程中的动态使用的鉴定。我们将pri-miRNA启动子分配给152种前体-miRNA（pre-miRNA），其中大多数得到启动子相关翻译后组蛋白修饰（H3 K4 me 3、H2 A. Z）和RNA聚合酶II（RNAPII）占用的支持。我们通过原位杂交验证了7个miR-9 pri-miRNAs，并显示出与成熟miR-9相似的表达模式。此外，通过5′ RACE PCR验证了miR-9-5内含子启动子的加工。发育分析揭示了母系遗传的pri-miRNAs的一个子集。此外，我们发现启动子相关的H3 K4 me 3，H2A.Z和RNAPII标记不仅存在于pri-miRNA启动子中，而且还特异性地富集在pre-miRNA中，表明pre-miRNA的染色质水平调节。此外，我们证明CAGE-seq还检测Drosha切割位点上的pre-miRNA的3′-末端加工，这与miRNA偏移RNA（莫尔纳斯）的产生相关，并提供了一种新的工具，用于检测Drosha加工事件并通过全基因组测定预测pre-miRNA加工。
MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes, especially in development and differentiation. Our understanding about the transcriptional regulation of miRNA genes is limited by inadequate annotation of primary miRNA (pri-miRNA) transcripts. Here, we used CAGE-seq and RNA-seq to provide genome-wide identification of the pri-miRNA core promoter repertoire and its dynamic usage during zebrafish embryogenesis. We assigned pri-miRNA promoters to 152 precursor-miRNAs (pre-miRNAs), the majority of which were supported by promoter associated post-translational histone modifications (H3K4me3, H2A.Z) and RNA polymerase II (RNAPII) occupancy. We validated seven miR-9 pri-miRNAs by in situ hybridization and showed similar expression patterns as mature miR-9. In addition, processing of an alternative intronic promoter of miR-9–5 was validated by 5′ RACE PCR. Developmental profiling revealed a subset of pri-miRNAs that are maternally inherited. Moreover, we show that promoter-associated H3K4me3, H2A.Z and RNAPII marks are not only present at pri-miRNA promoters but are also specifically enriched at pre-miRNAs, suggesting chromatin level regulation of pre-miRNAs. Furthermore, we demonstrated that CAGE-seq also detects 3′-end processing of pre-miRNAs on Drosha cleavage site that correlates with miRNA-offset RNAs (moRNAs) production and provides a new tool for detecting Drosha processing events and predicting pre-miRNA processing by a genome-wide assay.