An overview of microRNAs

doi:10.1016/j.addr.2015.05.001

Advanced Drug Delivery Reviews

Volume 87, 29 June 2015, Pages 3-14

https://doi.org/10.1016/j.addr.2015.05.001 Get rights and content

Abstract

The discovery of the first microRNA (miRNA) over 20 years ago has ushered in a new era in molecular biology. There are now over 2000 miRNAs that have been discovered in humans and it is believed that they collectively regulate one third of the genes in the genome. miRNAs have been linked to many human diseases and are being pursued as clinical diagnostics and as therapeutic targets. This review presents an overview of the miRNA pathway, including biogenesis routes, biological roles, and clinical approaches.

Graphical abstract

Section snippets

miRNAs are small noncoding regulatory RNAs

The first miRNA was discovered over 30 years ago in the nematode Caenorhabditis elegans with the identification of the developmental regulator lin-4 [1]. Originally believed to be a conventional protein coding gene, the Ruvkun and Ambros labs made the startling discovery that lin-4 did not code for a protein but instead coded for a 22 nucleotide regulatory RNA [2], [3]. They demonstrated that the lin-4 RNA could base pair with the mRNA for another gene in the C. elegans developmental network,

The canonical miRNA biogenesis pathway

All miRNA families undergo a series of biogenesis steps that convert the primary miRNA transcript into the active, ~ 22 nucleotide mature miRNA (see Fig. 1). The mature miRNA is loaded into the RNA induced silencing complex (RISC) where it directs the complex to target mRNAs, leading to translational repression and target mRNA degradation. This section will cover the canonical miRNA biogenesis pathway that is responsible for the maturation of most miRNA families. For simplicity we will focus on

miRNA target identification

Defining target sets for miRNAs is important for several reasons. For biologists, defining the target set of a miRNA is key to understanding its biological role. For scientists developing miRNA therapeutics, validated targets provide the best biomarker(s) for determination of the efficacy of a miRNA mimic or inhibitor. The identification of miRNA targets has followed three general approaches: bioinformatic target prediction, biochemical isolation of miRNA/mRNA complexes, and

Regulation of the miRNA pathway

Early work in the field focused on transcriptional regulation of miRNA host genes [25], [26], [117], [118]. For example, the cardiac-specific miRNA families miR-1 and miR-133 are transcriptionally regulated by well established cardiomyocyte transcription factor networks via SRF, MEF2, and MyoD [119], [120], [121], [122], [123]. Accordingly, enhancer elements for these factors have been identified in upstream regions of the miR-1/133 host genes. Similarly, miRNAs that are located in introns of

Biological roles of miRNAs

The biological importance of miRNAs in mammalian development was first demonstrated with the generation of mouse models deficient for Dicer and DGCR8 (Drosha is involved in other RNA metabolic pathways while DGCR8 is specific for miRNA biogenesis, thus the DGCR8 knockout is more informative). Loss of either step in miRNA biogenesis results in embryonic lethality [140], [141]. Similarly, tissue-specific knockout of either gene leads to developmental defects in that tissue, underscoring the

Dysregulation of miRNAs in disease

Gene expression profiling studies have demonstrated alterations in miRNA expression in a wide range of human disease. In many cases, functional studies have linked miRNA dysregulation as a causal factor in disease progression. This section will summarize some of the disease states that have been linked to miRNA alterations.

miRNAs as diagnostic markers

The extensive alterations in miRNA expression in disease provide great potential for clinical diagnostics based on miRNA signatures. Furthermore, miRNAs are more stable than mRNAs and can be recovered from formalin fixed paraffin sections (FFPE) and other sources with low overall RNA quality [198], [199], [200]. Current focus is on developing miRNA signatures for disease diagnosis, identifying cancers of unknown primary, and predicting response to therapy and drug resistance [201], [202], [203]

miRNAs as therapeutic targets

As miRNAs become causally linked to increasing numbers of human diseases there are expanding efforts to develop therapeutics that directly target the miRNA [234], [235], [236]. These candidates are either miRNA mimics or antisense inhibitors, depending on the miRNA and underlying therapeutic goal. These drug candidates are based on modified nucleic acids and therefore present delivery challenges. The most promising candidate to date is the Regulus drug RG-101, currently in Phase II trials [197]

Genome editing approaches

The miRNA pathway is a subset of post-transcriptional gene silencing (PTGS) pathways. In these related biological pathways the mRNA is the target of the silencing machinery, hence “post-transcriptional” silencing. A complementary approach to silence gene expression is to target the genome itself. Several approaches have been developed to redirect an endonuclease to a desired target site in genomic DNA [246]. The resultant double strand break is repaired, usually by non-homologous end joining,

Conclusion

We are entering an exciting time in the field of miRNA research. A decade of strong basic science research has forged links between specific miRNA alterations and many human diseases. We are now entering a phase where miRNA diagnostics and therapeutics can be developed with confidence, and several commercial efforts are underway to bring these developments to the clinic.

Acknowledgments

Work performed in the author's lab was supported by funding from the NIH (R01GM070674, RC1HL100108) and the Department of Cell Biology and Physiology.

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^☆: This review is part of the Advanced Drug Delivery Reviews theme issue on “ Oligonucleotide Therapeutics”.

View full text

An overview of microRNAs☆

Abstract

Graphical abstract

Section snippets

miRNAs are small noncoding regulatory RNAs

The canonical miRNA biogenesis pathway

miRNA target identification

Regulation of the miRNA pathway

Biological roles of miRNAs

Dysregulation of miRNAs in disease

miRNAs as diagnostic markers

miRNAs as therapeutic targets

Genome editing approaches

Conclusion

Acknowledgments

Cell

Cell

Cell

Cell

Cell

Cell

J. Biol. Chem.

Cell

Mol. Cell

Mol. Cell

Cell

J. Lipid Res.

Cell

Cell

Mol. Cell

Science

Cell

Curr. Biol.

Cell

Mol. Cell

Mol. Cell

Cell

Mol. Cell

Mol. Cell

Cell

Cell

Mol. Cell

Cell

Cell

Cell

J. Biol. Chem.

Isolation and genetic characterization of cell-lineage mutants of the nematode Caenorhabditis elegans

Genetics

The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans

Nature

Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA

Nature

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Nature

A species of small antisense RNA in posttranscriptional gene silencing in plants

Science

An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells

Nature

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA

Science

Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans

Genes Dev.

miRBase: microRNA sequences, targets and gene nomenclature

Nucleic Acids Res.

Identification of mammalian microRNA host genes and transcription units

Genome Res.

Identification of the miR-106b ~ 25 microRNA cluster as a proto-oncogenic PTEN-targeting intron that cooperates with its host gene MCM7 in transformation

Sci. Signal.

Identification of novel genes coding for small expressed RNAs

Science

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans

Science

An extensive class of small RNAs in Caenorhabditis elegans

Science

The database of experimentally supported targets: a functional update of TarBase

Nucleic Acids Res.

MicroRNA genes are transcribed by RNA polymerase II

EMBO J.

C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts

Nucleic Acids Res.