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  • Review Article
  • Published:

Endogenous microRNA sponges: evidence and controversy

Key Points

  • The competitive endogenous RNA (ceRNA) hypothesis posits that transcripts with shared microRNA binding sites compete for post-transcriptional control.

  • Experimental evidence is accumulating that describes ceRNA function for long non-coding RNAs, pseudogene transcripts, circular RNAs, viral RNAs as well as protein-coding transcripts.

  • Studies that quantitatively model transcriptome-wide ceRNA networks are challenging claims of the scale and potential effects of the ceRNA mechanism for individual transcripts.

  • Methodological limitations to both experimental and in silico evidence are explored to provide an objective assessment of the implications of the ceRNA hypothesis.

Abstract

The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.

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Figure 1: The competitive endogenous RNA mechanism.
Figure 2: The active transcriptome available for microRNA binding competition.
Figure 3: Strategies used to assess transcriptome-wide competition for microRNA binding.
Figure 4: Schematic of relative cellular abundance of microRNAs and predicted target sites.

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Acknowledgements

The authors thank E. Harvey and K. Patterson for figure preparation, also B. Signal and the Dinger laboratory for useful discussion.

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Correspondence to Marcel E. Dinger.

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Glossary

Long non-coding RNAs

(lncRNAs). Transcripts with little or no protein-coding potential that are greater than 200 nucleotides in length.

Competitive endogenous RNA

(ceRNA). RNA that leads to upregulation of expression of a target gene by competing for microRNA binding sites.

MicroRNA

(miRNA). A small (20–22 nucleotide long) non-coding RNA that inhibits gene expression by guiding the RNA-induced silencing complex (RISC) to target genes.

Pseudogene

A duplicated gene, identified through DNA homology to its parent gene but with evolutionarily acquired mutations.

Circular RNAs

(circRNAs). A class of RNAs derived mostly from non-canonical splicing in which the exon ends are joined to form a loop.

Antisense RNA

The reverse complement of a specified RNA. This differs from an antisense transcript, which refers to endogenous antisense transcription of an annotated gene.

ceRNA networks

(competitive endogenous RNA networks). Networks of interactions that arise from the concept that a collective pool of transcripts can synergistically compete for microRNA (miRNA) binding and that a single miRNA can silence several targets.

miRNA recognition elements

(MREs). MicroRNA (miRNA) binding sites that are canonically found in the 3′ untranslated region of a target mRNA and have sequence similarity to the 5′ seed region of the miRNA.

miRNA sponges

Antisense RNA transcripts that inhibit microRNA (miRNA) activity. These molecules can be artificially introduced or, if endogenous, are equivalent to competitive endogenous RNAs.

3′ untranslated regions

(3′ UTRs). The ends of messenger RNAs that follow the stop codon.

Dicer

A key protein in the microRNA (miRNA) and small interfering RNA (siRNA) biosynthesis pathways. Dicer is an endonuclease that cleaves double-stranded RNA and miRNA precursor transcripts.

RNA-induced silencing complex

(RISC). A protein complex that uses a single stranded guide RNA (for example, a microRNA (miRNA) or small interfering RNA (siRNA)) to elicit post-transcriptional gene silencing.

Argonaute

(AGO). A family of proteins that bind a guide RNA as part of the microRNA (miRNA) or small interfering RNA (siRNA) pathway.

HITS–CLIP

(High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation). A sequencing method to identify microRNA (miRNA) targets and functional miRNAs.

Small nuclear RNAs

(snRNAs). A class of nuclear localized RNAs with roles in splicing and RNA modification.

SILAC

(Stable isotope labelling by amino acids in cell culture). A proteomic approach using quantitative mass spectrometry.

Polysome profiling

The analysis of mRNAs associated with elongating ribosomes to identify translationally active mRNAs.

Centred pairing

A non-canonical mechanism of microRNA (miRNA) targeting in which six or more nucleotides in the centre of the miRNA bind target genes.

G-bulge

MicroRNA (miRNA) targeting of complementary nucleotides where a guanosine (G) nucleotide is skipped resulting in a 'bulge'.

Encyclopedia of DNA Elements

(ENCODE). An international consortium with the goal to build a comprehensive list of functional elements in the human genome.

Sensor-seq

A high-throughput assay of microRNA (miRNA) activity as measured by high-throughput sequencing of a pool of reporter constructs each with binding sites for individual miRNAs.

Individual-nucleotide resolution CLIP

(iCLIP). A crosslinking immunoprecipitation (CLIP) technique for identifying protein–RNA interactions, in which the direct crosslinking site can be identified where the reverse transcribed cDNA is truncated.

Pathway divergence

A signalling pathway that is amplified when signals from the same ligand activate a variety of different effectors leading to diverse cellular responses.

Small interfering RNA

(siRNA). siRNAs, which are also called silencing RNAs, act within the RNA-induced silencing complex (RISC) to guide gene silencing. The term can refer to a synthetic RNA duplex or an endogenously derived RNA from a double-stranded precursor.

CRISPR

A specific gene-editing technique using guide RNAs and CRISPR-associated protein 9 (Cas9).

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Thomson, D., Dinger, M. Endogenous microRNA sponges: evidence and controversy. Nat Rev Genet 17, 272–283 (2016). https://doi.org/10.1038/nrg.2016.20

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