The panorama of miRNA-mediated mechanisms in mammalian cells

Abstract

MicroRNAs comprise a large family of short, non-coding RNAs that are present in most eukaryotic organisms and are typically involved in downregulating the expression of protein-coding genes. The detailed mechanisms of miRNA functioning in animals and plants have been under investigation for more than decade. In mammalian cells, miRNA guides the effector complex miRISC to bind with partially complementary sequences, usually within the 3'UTR of mRNAs, and inhibit protein synthesis with or without transcript degradation. In addition to these main mechanisms, several other modes of miRNA-mediated gene expression regulation have been described, but their scale and importance remain a matter of debate. In this review, we briefly summarize the pathway of miRNA precursor processing during miRNA biogenesis and continue with the description of the miRISC assembly process. Then, we present the miRNA-mediated mechanisms of gene expression regulation in detail, and we gather information concerning the proteins involved in these processes. In addition, we briefly refer to the current applications of miRNA mechanisms in therapeutic strategies. Finally, we highlight some of the remaining controversies surrounding the regulation of mammalian gene expression by miRNAs.

Fig. 1

miRNA biogenesis in human cells. a The canonical pathway covers 1 pri-miRNA transcription, 2 Drosha cleavage, 3 pre-miRNA export to cytoplasm and 4 Dicer cleavage into 5 the miRNA/miRNA* duplex. b The alternative Drosha-independent biogenesis pathway (mirtron pathway) is indicated by the orange dashed line. See text for more details

Fig. 2

miRISC assembly in human cells. a The first step is miRISC loading, when the miRNA/miRNA* duplex is transferred from Dicer to Ago in the miRISC loading complex (RLC). b Next, domain N of Ago actively wedges between miRNA strands and c the PAZ domain of Ago unwinds the miRNA duplex. d The passenger strand is removed from miRISC and undergoes rapid degradation. e miRNA within mature miRISC binds with imperfect complementarity to its target sites. See text for more details

Fig. 3

The miRNA-binding site distribution in the mammalian transcriptome as revealed by different global analyses of RNAs immunoprecipitated with Ago proteins. The method, reference and experimental basics are given for each analysis. The main miRNA targets are found in mRNAs and were mapped to 5′UTR, CDS and 3′UTR regions (approximate shares of these reads are given in the pie charts). A group of “other” reads contains different non-coding RNAs: pseudogenes, intronic and intragenic sequences

Fig. 4

miRNA-mediated mechanism of gene expression regulation in human cells. Mature miRISC binds miRNA target sites localized I mostly within the 3′UTR but also (indicated in orange) II in the 5′UTR or III in the CDS. There are two main pathways of miRNA-mediated mechanisms of gene expression regulation: a translation inhibition either on initiation (1, 2) or at a post-initiation step (3–5) and b deadenylation followed by c decapping and d, e mRNA decay. However, some less well-known alternatives, indicated by dashed orange lines, have been described: f translation upregulation, g import into the nucleus and h alternative splicing modulation, i decapping followed by translation inhibition and j deadenylation followed by translation inhibition. See text for more details