Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Molecular Engineering Laboratory, A★STAR, Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Mol Cell. 2018 Mar 15;69(6):1005-1016.e7. doi: 10.1016/j.molcel.2018.02.012.
RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced UV crosslinking followed by immunoprecipitation (eCLIP) datasets for 126 RBPs to discover miR-encoding genomic loci that are statistically enriched for RBP binding. We find that 92% of RBPs interact directly with at least one miR locus, and that some interactions are cell line specific despite expression of the miR locus in both cell lines evaluated. We validated that ILF3 and BUD13 directly interact with and stabilize miR-144 and that BUD13 suppresses mir-210 processing to the mature species. We also observed that DDX3X regulates primary miR-20a, while LARP4 stabilizes precursor mir-210. Our approach to identifying regulators of miR loci can be applied to any user-defined RNA annotation, thereby guiding the discovery of uncharacterized regulators of RNA processing.
RNA 结合蛋白（RBPs）与初级、前体和成熟 microRNAs（miRs）相互作用，影响成熟 miR 的水平，进而影响人类发育和疾病的关键方面。为了了解 RBPs 如何促进 miR 生物发生，我们分析了 126 种 RBP 的人类增强紫外线交联后免疫沉淀（eCLIP）数据集，以发现 miR 编码基因组座，这些基因组座在统计学上富含 RBP 结合。我们发现 92%的 RBPs 直接与至少一个 miR 基因座相互作用，并且尽管在评估的两种细胞系中都表达了 miR 基因座，但一些相互作用是细胞系特异性的。我们验证了 ILF3 和 BUD13 直接相互作用并稳定 miR-144，并且 BUD13 抑制 mir-210 向成熟体的加工。我们还观察到 DDX3X 调节初级 miR-20a，而 LARP4 稳定前体 mir-210。我们识别 miR 基因座调节剂的方法可以应用于任何用户定义的 RNA 注释，从而指导对 RNA 加工的未表征调节剂的发现。
