miRNA-independent function of long noncoding pri-miRNA loci
miRNA-independent function of long noncoding pri-miRNA loci
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DOI：
10.1073/pnas.2017562118
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发表时间：
2021-03-30
影响因子：
11.1
通讯作者：
Lim, Daniel A.
中科院分区：
文献类型：
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作者：
He, Daniel;Wu, David;Lim, Daniel A.
在大量多样的哺乳动物长链非编码rna （lncrna）中，长链非编码初级microrna （lnc-pri- mirna）是宿主mirna的microrna。lnc-pri-miRNA位点是否具有独立于其同源mirna的重要生物学功能尚不清楚。从基因组尺度的lncRNA筛选中，lnc-pri-miRNA位点在细胞增殖中富集，并且在DGCR8或DROSHA敲低的胶质母细胞瘤（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位点的功能，我们研究了承载miR-29a/b1簇的LOC646329（也称为MIR29HG）。在GBM细胞中，LOC646329敲低降低了miR-29a/b1水平，这些细胞表现出生长下降。然而，基因缺失miR-29a/b1簇（LOC646329-miR29 Delta）并不会降低细胞生长，而敲低LOC646329-miR29 Delta转录本则会降低细胞增殖。LOC646329的miR-29a/b1独立活性对应于邻近癌基因（MKLN1）的增强子样激活，从而调节细胞增殖。LOC646329位点与MKLN1启动子相互作用，lncRNA的反义寡核苷酸敲低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位点在与基因启动子的DNA环相互作用以及转录增强子的基因组和表观遗传特征中显著富集。其他lnc-pri-miRNA位点的功能研究显示同源的mirna非依赖性增强子样活性。总之，这些数据表明lnc-pri-miRNA位点可以通过mirna依赖和mirna不依赖的机制调节细胞生物学。
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 DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29 Delta) did not decrease cell growth, while knockdown of LOC646329-miR29 Delta transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 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.