miRNA-independent function of long noncoding pri-miRNA loci.

Abstract

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 <i>DGCR8</i> or <i>DROSHA</i> knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied <i>LOC646329</i> (also known as <i>MIR29HG</i>), which hosts the miR-29a/b1 cluster. In GBM cells, <i>LOC646329</i> knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (<i>LOC646329-miR29Δ</i>) did not decrease cell growth, while knockdown of <i>LOC646329-miR29Δ</i> transcripts reduced cell proliferation. The miR-29a/b1-independent activity of <i>LOC646329</i> corresponded to enhancer-like activation of a neighboring oncogene (<i>MKLN1</i>), regulating cell propagation. The <i>LOC646329</i> locus interacts with the <i>MKLN1</i> 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.