The role of miRNAs in regulating gene expression networks

Abstract

MicroRNAs (miRNAs) are key regulators of gene expression. They are conserved across species, expressed across cell types, and active against a large proportion of the transcriptome. The sequence-complementary mechanism of miRNA activity exploits combinatorial diversity, a property conducive to network-wide regulation of gene expression, and functional evidence supporting this hypothesized systems-level role has steadily begun to accumulate. The emerging models are exciting and will yield deep insight into the regulatory architecture of biology. However, because of the technical challenges facing the network-based study of miRNAs, many gaps remain. Here, we review mammalian miRNAs by describing recent advances in understanding their molecular activity and network-wide function.

Keywords: Ago2; Argonaute 2; Dicer; Drosha; EMT; ESC; KO; RISC; RNA-induced silencing complex; TGFβ; UTR; embryonic stem cell; epithelial-to-mesenchymal transition; knockout; let-7; miRNA; microRNA; network; pre-miRNA; precursor miRNA; transforming growth factor beta; untranslated region.

Figure 1

The miRNA biogenesis pathway. MiRNA genes are transcribed by RNA Polymerase II, in combination with specific transcription factors (TF), as long primary transcripts (pri-miRNA). These transcripts are then processed in the nucleus by the RNase III enzyme Drosha, in complex with DGCR8, into precursor miRNAs (pre-miRNA), which are exported into the cytoplasm by Exportin 5. Pre-miRNAs are processed by the RNase III enzyme Dicer, in complex with TRBP, into a duplex consisting of a guide strand (miRNA) and passenger star strand (miRNA*). The mature miRNA is loaded into the RNA-induced silencing complex (RISC) and acts as a guide strand that recognizes target mRNAs based on sequence complementarity. The RISC subsequently represses targets by inhibiting translation or promoting destabilization of target mRNAs.

Figure 2

Crystal structure of human Argonaute 2 in complex with miR-20a. Ago2 is a bilobed protein with a multidomain conformation. The guide RNA is anchored at the ends by each lobe, with the MID domain binding the 5’-end, and the PAZ domain binding the 3’-end. Bases within the seed of the guide strand are solvent exposed, with a kink between nucleotides 6 and 7. The crystal structure shown (Protein Data Bank ID 4F3T) was reported by Elkayam and colleagues.

Figure 3

Embryonic stem cell-specific miRNAs. (A) Gene structure of the murine miR-290~295 and miR-302~367 clusters. The pre-miRNA sequences are indicated as boxes, with mature miRNA sequences denoted in darker shades. Related family members are indicated by color. (B) Sequences of miRNAs. Each miRNA is grouped based on seed relationship. Seeds are bold and underlined. (C) Summary of the miR-290~295 network.

Figure 4

The let-7 genes. (A) Gene structure of the let-7 genes. At three loci, let-7 is clustered with the miR-99/100 and miR-125 families. The pre-miRNA sequences are indicated as boxes, with mature miRNA sequences denoted in darker shades. Related family members are indicated by color. (B) Sequences of miRNAs. Each miRNA is grouped based on seed relationship. Seeds are bold and underlined. (C) Summary of the let-7 network. Let-7 genes are characterized by a shared role in regulating proliferative and metabolic pathways activated in the embryo. Let-7 targets are densely interconnected and regulate one another.

Figure 5

The miR-17~92 genes. (A) Gene structure of paralogues miR-17~92, miR-106a~363, and miR-106b~25. The pre-miRNA sequences are indicated as boxes, with mature miRNA sequences denoted in darker shades. Related family members are indicated by color. (B) Sequences of miRNAs. Each miRNA is grouped based on seed relationship. Seeds are bold and underlined. (C) Summary of the miR-17~92 network.

Figure 6

The miR-34 and miR-449 genes. (A) Gene structure of miR-34a, miR-34b~34c, and miR-449c~449a. The pre-miRNA sequences are indicated as boxes, with mature miRNA sequences denoted in in darker shades. Related family members are indicated by color. miR-34 and miR-449 share the same seed sequence. (B) Sequences of miRNAs. Each miRNA is grouped based on seed relationship and sequence similarity. Seeds are bold and underlined. (C) Summary of the miR-34 network.