A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

Abstract

SUMMARYNoncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs-a long ncRNA, a circular RNA, and two microRNAs-using gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more efficient than previously described examples of target-directed microRNA degradation, which come from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7-targeted mRNAs and enables the accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network. HIGHLIGHTSA long noncoding RNA, a circular RNA, and two microRNAs form a regulatory network The Cyrano long noncoding RNA directs potent, multiple-turnover destruction of miR-7

Past, present, and future of circ RNA s

“…A first hint for circRNA degradation via endonuclease activity has been shown using RNase H and Rrp44 in vitro (Mackie, 1998;Schaeffer et al, 2009). CDR1as, miR-671, and its binding site are highly conserved (Hansen et al, 2013), and the deletion of this site results in a significant increase in CDR1as levels (Kleaveland et al, 2018). Small RNA-mediated degradation of circRNAs is so far the best characterized circRNA degradation pathway.…”

“…In both cases, the authors tested artificial circular RNA constructs and cleavage of these circRNA species was very low. Interestingly, CDR1as levels are modulated by miR-7 likely through slicing, which is also dependent on miR-671 (Kleaveland et al, 2018). However, the only example until now, besides artificial shRNA/siRNA-based systems (Jeck et al, 2013;Legnini et al, 2017;Pamudurti et al, 2017;Yu et al, 2017), is the degradation of CDR1as by miR-671 (Hansen et al, 2011).…”

“…circRNA as modulators of miRNA function Some long non-coding RNAs can regulate miRNA levels and/or activity by selective sponging (Cesana et al, 2011;Tay et al, 2011;Bitetti et al, 2018;Kleaveland et al, 2018). The initial observation that some circRNA possess many miRNA-binding sites led to the speculation that these molecules could work as miRNA sponges.…”

“…Recent work showed that CDR1as is part of an even more complex regulatory circuit that involves the long intergenic noncoding RNA (lincRNA) Cyrano (Kleaveland et al, 2018). By generating and using different CRISPR-Cas9 engineered mice, Kleaveland et al (2018) show that Cyrano binds and targets miR-7 for degradation.…”

“…Two studies investigated the role of CDR1as in vivo (Piwecka et al, 2017;Kleaveland et al, 2018). Although this circRNA is embedded in a long non-coding RNA locus (Barrett et al, 2017), the circularization of CDR1as is so efficient that previous studies could not detect any linear counterpart (Hansen et al, 2011(Hansen et al, , 2013Memczak et al, 2013).…”