Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation

Abstract

Little is known about miRNA decay. A target-directed miRNA degradation mechanism (TDMD) has been suggested, but further investigation on endogenous targets is necessary. Here, we identify hundreds of targets eligible for TDMD and show that an endogenous RNA (Serpine1) controls the degradation of two miRNAs (miR-30b-5p and miR-30c-5p) in mouse fibroblasts. In our study, TDMD occurs when the target is expressed at relatively low levels, similar in range to those of its miRNAs (100–200 copies per cell), and becomes more effective at high target:miRNA ratios (>10:1). We employ CRISPR/Cas9 to delete the miR-30 responsive element within Serpine1 3'UTR and interfere with TDMD. TDMD suppression increases miR-30b/c levels and boosts their activity towards other targets, modulating gene expression and cellular phenotypes (i.e., cell cycle re-entry and apoptosis). In conclusion, a sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets exists in mammalian cells.

miR‐29c improves skeletal muscle mass and function throughout myocyte proliferation and differentiation and by repressing atrophy‐related genes

“…In fact, it has been described that target RNAs can function as miR sponges . After a particular miR binds to the target mRNA, the mRNA can be degraded along with the miR …”

Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation

“…89,90 Because human and, in general, metazoan genomes seem to lack highly complementary miRNA binding sites that would trigger cellular TDMD, its physiological relevance remained into question until recently. After the identification of miR-29b as the only member of the miR-29 family associated with TDMD in the cerebellum of zebrafish by the presence of endogenous libra lnc-RNA, or in mice by expression of the homolog Nrep transcript encoding a small protein, 91 additional TDMD examples have been described. Interestingly, disruption of miR-29b degradation leads to anxiety-like behaviors in both organisms, arguing in favor of a regulatory TDMD pathway in vertebrates.…”

How Complementary Targets Expose the microRNA 3′ End for Tailing and Trimming during Target-Directed microRNA Degradation

“…Despite this protection, miRNA stability varies greatly (Duffy et al 2015;Marzi et al 2016), and miRNA levels are tightly regulated (e.g., during development or the cell cycle [Monticelli et al 2005;Rissland et al 2011]). But the mechanisms of miRNA regulation are not well-understood and only two miRNA decay pathways have been described: Tudor SN-mediated miRNA decay (TumiD) (Elbarbary et al 2017) and target-directed miRNA degradation (TDMD) (Ameres et al 2010;Baccarini et al 2011;Libri et al 2012;Marcinowski et al 2012;Lee et al 2013;Bitetti et al 2018;Cazalla 2018;Ghini et al 2018;Kleaveland et al 2018). TDMD is the subject of this review.…”