Scheller Ute, Pfisterer Kathrin, Uebe Steffen, Ekici Arif B, Reis André, Jamra Rami, Ferrazzi Fulvia
Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054, Erlangen, Germany.
Institute of Human Genetics, University of Leipzig, Philipp-Rosenthal-Straße 55, 04103, Leipzig, Germany.
BMC Med Genomics. 2018 Apr 23;11(1):41. doi: 10.1186/s12920-018-0358-6.
Decapping of mRNA is an important step in the regulation of mRNA turnover and therefore of gene expression, which is a key process controlling development and homeostasis of all organisms. It has been shown that EDC3 plays a role in mRNA decapping, however its function is not well understood. Previously, we have associated a homozygous variant in EDC3 with autosomal recessive intellectual disability. Here, we investigate the functional role of EDC3.
We performed transcriptome analyses in patients' samples. In addition, we established an EDC3 loss-of-function model using siRNA-based knockdown in the human neuroblastoma cell line SKNBE and carried out RNA sequencing. Integrative bioinformatics analyses were performed to identify EDC3-dependent candidate genes and/or pathways.
Our analyses revealed that 235 genes were differentially expressed in patients versus controls. In addition, AU-rich element (ARE)-containing mRNAs, whose degradation in humans has been suggested to involve EDC3, had higher fold changes than non-ARE-containing genes. The analysis of RNA sequencing data from the EDC3 in vitro loss-of-function model confirmed the higher fold changes of ARE-containing mRNAs compared to non-ARE-containing mRNAs and further showed an upregulation of long non-coding and coding RNAs. In total, 764 genes were differentially expressed. Integrative bioinformatics analyses of these genes identified dysregulated candidate pathways, including pathways related to synapses/coated vesicles and DNA replication/cell cycle.
Our data support the involvement of EDC3 in mRNA decay, including ARE-containing mRNAs, and suggest that EDC3 might be preferentially involved in the degradation of long coding and non-coding RNAs. Furthermore, our results associate ECD3 loss-of-function with synapses-related pathways. Collectively, our data provide novel information that might help elucidate the molecular mechanisms underlying the association of intellectual disability with the dysregulation of mRNA degradation.
mRNA脱帽是调节mRNA周转进而调控基因表达的重要步骤，而基因表达是控制所有生物体发育和体内平衡的关键过程。已有研究表明EDC3在mRNA脱帽过程中发挥作用，但其功能尚未完全明确。此前，我们发现EDC3中的一个纯合变异与常染色体隐性智力障碍有关。在此，我们对EDC3的功能作用展开研究。
我们对患者样本进行了转录组分析。此外，我们利用基于小干扰RNA（siRNA）的敲低技术在人神经母细胞瘤细胞系SKNBE中建立了EDC3功能缺失模型，并进行了RNA测序。通过综合生物信息学分析来鉴定EDC3依赖性候选基因和/或通路。
我们的分析显示，与对照组相比，患者中有235个基因表达存在差异。此外，富含AU元件（ARE）的mRNA（其在人类中的降解被认为与EDC3有关）的倍数变化高于不含ARE的基因。对EDC3体外功能缺失模型的RNA测序数据进行分析，证实了与不含ARE的mRNA相比，含ARE的mRNA具有更高的倍数变化，并且进一步显示长链非编码RNA和编码RNA上调。总共764个基因表达存在差异。对这些基因进行综合生物信息学分析，确定了失调的候选通路，包括与突触/被膜小泡以及DNA复制/细胞周期相关的通路。
我们的数据支持EDC3参与mRNA衰变，包括含ARE的mRNA，并表明EDC3可能优先参与长链编码和非编码RNA的降解。此外，我们的结果将EDC3功能缺失与突触相关通路联系起来。总体而言，我们的数据提供了新的信息，可能有助于阐明智力障碍与mRNA降解失调之间关联的分子机制。
