Hinske Ludwig Christian, Galante Pedro A F, Limbeck Elisabeth, Möhnle Patrick, Parmigiani Raphael B, Ohno-Machado Lucila, Camargo Anamaria A, Kreth Simone
Research Group Molecular Medicine, Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany.
Molecular Oncology Center, Sírio Libanês Hospital, São Paulo, Brazil.
PLoS One. 2015 Mar 23;10(3):e0121507. doi: 10.1371/journal.pone.0121507. eCollection 2015.
About half of the known miRNA genes are located within protein-coding host genes, and are thus subject to co-transcription. Accumulating data indicate that this coupling may be an intrinsic mechanism to directly regulate the host gene's expression, constituting a negative feedback loop. Inevitably, the cell requires a yet largely unknown repertoire of methods to regulate this control mechanism. We propose APA as one possible mechanism by which negative feedback of intronic miRNA on their host genes might be regulated. Using in-silico analyses, we found that host genes that contain seed matching sites for their intronic miRNAs yield longer 32UTRs with more polyadenylation sites. Additionally, the distribution of polyadenylation signals differed significantly between these host genes and host genes of miRNAs that do not contain potential miRNA binding sites. We then transferred these in-silico results to a biological example and investigated the relationship between ZFR and its intronic miRNA miR-579 in a U87 cell line model. We found that ZFR is targeted by its intronic miRNA miR-579 and that alternative polyadenylation allows differential targeting. We additionally used bioinformatics analyses and RNA-Seq to evaluate a potential cross-talk between intronic miRNAs and alternative polyadenylation. CPSF2, a gene previously associated with alternative polyadenylation signal recognition, might be linked to intronic miRNA negative feedback by altering polyadenylation signal utilization.
已知的 miRNA 基因中约有一半位于蛋白质编码宿主基因内，因此会进行共转录。越来越多的数据表明，这种偶联可能是直接调控宿主基因表达的一种内在机制，构成一个负反馈环。不可避免地，细胞需要一套很大程度上未知的方法来调控这种控制机制。我们提出 APA 作为一种可能的机制，通过它可以调控内含子 miRNA 对其宿主基因的负反馈。通过计算机分析，我们发现其内含子 miRNA 具有种子匹配位点的宿主基因会产生更长的 3′UTR，且具有更多的聚腺苷酸化位点。此外，这些宿主基因与不含潜在 miRNA 结合位点的 miRNA 宿主基因之间，聚腺苷酸化信号的分布存在显著差异。然后我们将这些计算机分析结果应用到一个生物学实例中，在 U87 细胞系模型中研究了 ZFR 与其内含子 miRNA miR-579 之间的关系。我们发现 ZFR 被其内含子 miRNA miR-579 靶向，并且可变聚腺苷酸化允许差异靶向。我们还使用生物信息学分析和 RNA 测序来评估内含子 miRNA 与可变聚腺苷酸化之间的潜在相互作用。CPSF2 是一个先前与可变聚腺苷酸化信号识别相关的基因，它可能通过改变聚腺苷酸化信号的利用与内含子 miRNA 负反馈相关联。
