miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA

Abstract

MicroRNAs (miRNAs) are B22 nt non-coding RNAs that typically bind to the 3 0 UTR of target mRNAs in the cytoplasm, resulting in mRNA destabilization and translational repression. Here, we report that miRNAs can also regulate gene expression by targeting non-coding antisense transcripts in human cells. Specifically, we show that miR-671 directs cleavage of a circular antisense transcript of the Cerebellar Degeneration-Related protein 1 (CDR1) locus in an Ago2-slicer-dependent manner. The resulting downregulation of circular antisense has a concomitant decrease in CDR1 mRNA levels, independently of heterochromatin formation. This study provides the first evidence for non-coding antisense transcripts as functional miRNA targets, and a novel regulatory mechanism involving a positive correlation between mRNA and antisense circular RNA levels.

CiRS‐7 targeting miR‐7 modulates the progression of non‐small cell lung cancer in a manner dependent on NF‐κB signalling

“…Hence, circRNAs were more likely to be implicated within the mechanisms that gave rise to dysfunctional bioactivities, such as the onset and aggravation of cancers. For instance, ciRS‐7, the natural antisense transcript of cerebellar degeneration‐associated protein 1 (CRD1), contained approximately 70 MREs of miR‐7 24, 32, 36. Its high expression within cytoplasms could effectively lower miR‐7 activity through binding to it, thereby down‐regulating the expressions of insulin‐like growth factor‐1 receptor (IGF1R), epidermal growth factor receptor (EGFR) and focal adhesion kinase (FAK) 37, 38, 39…”

Nuclear microRNAs and their unconventional role in regulating non-coding RNAs

“…In addition, Weinmann et al detected AGO2 in the nucleus of HeLa cells (Weinmann et al, 2009). Notably, it has been shown that Argonaute proteins are directly associated with nuclear miRNAs in Caenorhabditis elegans (C. elegans) (Zisoulis et al, 2012) and human cells (Hansen et al, 2011;Zisoulis et al, 2012). Because Argonaute proteins are the catalytic center of RISC, their presence in the nucleus may imply that they have biological relevance in the nucleus.…”

“…The fi nding that significant amounts of mature miRNAs are localized in the nucleus (Meister et al, 2004;Politz et al, 2006;Hwang et al, 2007;Foldes-Papp et al, 2009;Liao et al, 2010;Jeffries et al, 2011) raises the interesting possibility that miRNAs may function as gene regulators in the nucleus, through a mechanism other than classic post-transcriptional repression. Indeed, recent studies by our (Tang et al, 2012) and other research groups (Hansen et al, 2011;Zisoulis et al, 2012) demonstrate that some miRNAs can act in an unconventional manner to regulate the biogenesis and function of ncRNAs, including miRNAs and long ncRNAs. These intriguing discoveries lead to a novel model of miRNA function and add new complexity to the gene regulatory network.…”

Circular RNAs: Unexpected outputs of many protein-coding genes

“…The CDR1as/ciRS-7 circular RNA contains a near perfect miR-671 target site that can be cleaved by Ago-2 to trigger transcript degradation. 56 This, however, appears to be an isolated mechanism, as no other circular RNA is known to contain similar sequences that induce Ago-2 slicing. Roles for other RNA endonucleases in circular RNA decay have not yet been explored.…”

“…This was the first hint that the dominant output of a gene could, in some cases, be a circular RNA rather than a linear mRNA. 48 A handful of additional circular RNAs were identified over the ensuing years [49][50][51][52][53][54][55][56] until deep sequencing efforts combined with new computational algorithms all of a sudden revealed thousands of previously missed circular RNAs from eukaryotic cells. 13,14,27,29,31,33,40,57,58 Over 25,000 putative circular RNAs, derived from »15% of actively transcribed genes, were identified in human fibroblasts alone.…”