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Diversifying microRNA sequence and function

Nature Reviews Molecular Cell Biology volume 14, pages 475–488 (2013)Cite this article

Subjects

Key Points

  • MicroRNAs (miRNAs) are small non-coding RNAs that guide post-transcriptional gene regulation to shape the rate at which genetic information is converted into proteins. Due to this, miRNAs contribute to the establishment of gene expression patterns that are required for normal development and physiology in plants and animals.

  • RNase III enzymes, together with specific double-stranded RNA-binding partner proteins, produce miRNAs from genomically encoded precursor miRNAs (pre-miRNAs). In rare cases, nucleases from other cellular pathways can replace RNase III enzymes in the production of miRNAs.

  • After the assembly of miRNA duplexes, these small RNAs are loaded into proteins from the Argonaute (AGO) protein family. AGO proteins organize small RNAs into subdomains, including the seed sequence, which mediates target RNA binding. The mechanisms by which miRNAs function include endonucleolytic cleavage, translational repression and mRNA turnover.

  • Recent evidence suggests that small RNA stability can be influenced by miRNA sequence motifs, chemical modifications and interactions with target mRNAs.

  • miRNAs are annotated as single sequences, but recent high-throughput efforts to catalogue small RNAs from various organisms, tissues and cell types reveal that most miRNAs comprise multiple isoforms. Several mechanisms have been shown to diversify miRNA sequence and function.

  • The advent of next-generation sequencing technology has revealed the miRNAs of key model organisms, but the extent to which each miRNA contributes to the regulation of targets in the transcriptome of a given cell type remains unclear. The biochemical and biophysical properties of miRNA silencing complexes provide a quantitative framework for their reciprocal function and their targets, according to their abundance and relative stoichiometry inside the cell.

Abstract

MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.

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Figure 1: MicroRNA biogenesis.
Figure 2: Small RNA turnover by tailing and trimming.
Figure 3: Mechanisms and consequences of microRNA isoforms.
Figure 4: microRNA function in plants and animals.
Figure 5: A quantitative framework for microRNA function.

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Acknowledgements

The authors thank the members of the Zamore and Ameres laboratories for helpful discussions and comments. The Ameres laboratory is funded by the Austrian Academy of Sciences and the Austrian Federal Ministry of Economy, Family and Youth (BMFWJ).

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Authors and Affiliations

  1. Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, Vienna, 1030, Austria

    Stefan L. Ameres

  2. Howard Hughes Medical Institute and University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, 01605, Massachusetts, USA

    Phillip D. Zamore

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  1. Stefan L. Ameres
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  2. Phillip D. Zamore
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Correspondence to Stefan L. Ameres or Phillip D. Zamore.

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Glossary

Argonaute

(AGO). Proteins that are guided to mRNA targets by small silencing RNAs. AGO proteins can also serve as scaffolds to bind secondary silencing factors such as the GW-repeat-containing protein GW182.

Primary miRNAs

(pri-miRNAs). Polyadenylated, 7-methylguanosine-capped RNA polymerase II transcripts containing a stem–loop structure that serves as a substrate for the RNase III enzyme Drosha in animals and Dicer-like 1 (DCL1) in plants. They are processed to liberate a precursor miRNA and two unstable, single-stranded by-products.

Ribonuclease III

(RNAse III). Double-stranded RNA-specific endoribonuclease that generates products with two nucleotide 3′ overhangs, a 5′ phosphate and a 3′ hydroxyl group.

dsRNA-binding protein

Proteins containing double-stranded RNA-binding domains, which are ∼70 amino acid motifs that bind to RNA helices via their 2′ hydroxyl group and phosphate backbone.

Precursor miRNAs

(pre-miRNAs). Stem–loop RNAs comprising a single-stranded loop that connects two partially complementary sequences. These sequences pair to form a predominantly double-stranded stem. Pre-miRNAs typically have a 5′ phosphate and a two nucleotide 3′ overhang, allowing them to serve as substrates for Dicer.

Drosha

The nuclear RNase III endonuclease in animals that cleaves the base of a stem–loop structure contained in primary microRNAs (pri-miRNAs) to produce a precursor miRNA. Collaborates with mammalian DGCR8 (or Pasha in other animals), which is its double-stranded RNA-binding protein partner.

Dicer

An RNase III endonuclease that is predominantly found in the cytoplasm of animal cells and the nucleus of plant and some fungal cells. Dicer proteins liberate mature microRNA–microRNA* duplexes from pre-microRNAs and siRNA duplexes from long double-stranded RNAs.

siRNAs

The ∼21 nucleotide small RNAs that mediate RNA interference in plants, animals and some fungi. Typically produced by Dicer processing of long double-stranded RNA (dsRNA) precursors encoded in the genome (endo-siRNAs) or from exogenous dsRNA sources (exo-siRNAs) such as viruses.

RNA-induced silencing complex

(RISC). A ribonucleoprotein complex that consists of a small RNA guide strand bound to an Argonaute protein. RISC mediates all RNA silencing pathways, and it can also include auxiliary proteins that extend or modify its function.

Seed sequence

A nucleotide motif in the 5′ domain of all small silencing RNAs, which is organized by Argonaute to determine target-RNA recognition.

PIWI-interacting RNAs

(piRNAs). Small silencing RNAs, 25–35 nucleotides long, that bind PIWI clade Argonaute proteins in animals and silence germline transposons. They are thought to derive from single-stranded RNA precursors and do not require RNase III enzymes for their maturation.

Exoribonuclease

Enzymes that successively remove nucleotides from either the 3′ (3′-to-5′ exoribonuclease) or the 5′ end (5′-to-3′ exoribonuclease) of RNA. They catalyse phosphodiester bond cleavage using water (releasing nucleotide monophosphates) or inorganic phosphate (releasing nucleotide diphosphates) as a nucleophile.

Isomirs

microRNA variants containing sequences that deviate from miRBase-annotated or most frequently observed species.

Mirtrons

Intron-derived precursor microRNAs excised from primary miRNAs by the splicing machinery and a lariat-debranching enzyme instead of Drosha.

Terminal nucleotidyl transferases

(TNTases). Template-independent polymerases that add nucleotides to the 3′ ends of nucleic acids.

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Ameres, S., Zamore, P. Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol 14, 475–488 (2013). https://doi.org/10.1038/nrm3611

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