Department of Neurological Surgery, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143.
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143.
Proc Natl Acad Sci U S A. 2021 Mar 30;118(13). doi: 10.1073/pnas.2017562118.
Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with or knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied (also known as ), which hosts the miR-29a/b1 cluster. In GBM cells, knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster () did not decrease cell growth, while knockdown of transcripts reduced cell proliferation. The miR-29a/b1-independent activity of corresponded to enhancer-like activation of a neighboring oncogene (), regulating cell propagation. The locus interacts with the promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.
在哺乳动物长非编码 RNA（lncRNA）的庞大而多样化的集合中，长非编码初级 microRNA（lnc-pri-miRNA）是那些包含 microRNA 的 RNA。lnc-pri-miRNA 基因座是否具有与其同源 microRNA 无关的重要生物学功能尚不清楚。从全基因组 lncRNA 筛选中，lnc-pri-miRNA 基因座富集了与细胞增殖相关的功能，并且在具有或 敲低的神经胶质瘤（即 GBM）细胞中，lnc-pri-miRNA 筛选命中仍然调节细胞生长。为了从分子上剖析 lnc-pri-miRNA 基因座的功能，我们研究了 （也称为 ），它包含 miR-29a/b1 簇。在 GBM 细胞中， 敲低降低了 miR-29a/b1 的水平，这些细胞的生长减少。然而，miR-29a/b1 簇的基因缺失（）并没有降低细胞生长，而 的转录本敲低则减少了细胞增殖。miR-29a/b1 非依赖性的 活性对应于邻近癌基因（）的增强子样激活，调节细胞增殖。 基因座与 启动子相互作用，反义寡核苷酸敲低 lncRNA 会破坏这些相互作用并降低增强子样活性。更广泛地说，对来自多种人类细胞类型的全基因组数据的分析表明，lnc-pri-miRNA 基因座与基因启动子以及转录增强子的基因组和表观遗传特征显著富集 DNA 环互作用。对其他 lnc-pri-miRNA 基因座的功能研究表明，其具有与 microRNA 无关的增强子样活性。总的来说，这些数据表明 lnc-pri-miRNA 基因座可以通过 microRNA 依赖和非依赖的机制来调节细胞生物学。
