In molecular biology, competing endogenous RNAs (abbreviated ceRNAs) regulate other RNA transcripts by competing for shared microRNAs (miRNAs). Models for ceRNA regulation describe how changes in the expression of one or multiple miRNA targets alter the number of unbound miRNAs and lead to observable changes in miRNA activity - i.e., the abundance of other miRNA targets. Models of ceRNA regulation differ greatly. Some describe the kinetics of target-miRNA-target interactions, where changes in the expression of one target species sequester one miRNA species and lead to changes in the dysregulation of the other target species. Others attempt to model more realistic cellular scenarios, where multiple RNA targets are affecting multiple miRNAs and where each target pair is co-regulated by multiple miRNA species. Some models focus on mRNA 3' UTRs as targets, and others consider long non-coding RNA targets as well. It's evident that our molecular-biochemical understanding of ceRNA regulation remains incomplete.
Hundreds of publications have described the influence of ceRNA regulation in normal and disease cells, but ceRNA regulation and its effects continue to be debated in scientific circles.
Summary
MicroRNAs are an abundant class of small, non-coding RNAs (~22nt long), which negatively regulate gene expression at the levels of messenger RNAs (mRNAs) stability and translation inhibition. The human genome contains over 1000 miRNAs, each one targeting hundreds of different genes. It is estimated that half of all genes of the genome are targets of miRNA, spanning a large layer of regulation on a post-transcriptional level. The seed region, which comprises nucleotides 2-8 of the 5' portion of the miRNA, is particularly crucial for mRNA recognition and silencing.
Recent studies have shown that the interaction of the miRNA seed region with mRNA is not unidirectional, but that the pool of mRNAs, transcribed pseudogenes, long noncoding RNAs (lncRNA), circular RNA (circRNA) compete for the same pool of miRNA thereby regulating miRNA activity. These competitive endogenous RNAs (ceRNAs) act as molecular sponges for a microRNA through their miRNA binding sites (also referred to as miRNA response elements, MRE), thereby de-repressing all target genes of the respective miRNA family. Experimental evidence for such a ceRNA crosstalk has been initially shown for the tumor suppressor gene PTEN, which is regulated by the 3' untranslated region (3'UTR) of the pseudogene PTENP1 in a DICER-dependent manner.
A new mechanism has recently been shown in which two closely spaced MREs (of the same or of different miRNA families) can cooperatively sequester miRNAs and thereby significantly boost a ceRNA effect. For a cooperative effect to be considered two adjacent MREs, however, have to be of miRNA families that are expressed high enough to actively repress targets and to be less than 58 nucleotides apart.
The biological relevance of the ceRNA hypothesis has been actively debated. Most notably, it has been challenged by a group of researchers that performed a quantitative assessment of two miRNA families (highly and lowly expressed) and their binding sites in liver- and embryonic stem cells as described below. However, these studies were focused on one miRNA per context, and their leading researchers later identified physiologically-relevant ceRNA regulation of another miRNA.
Debate on physiological relevance
Two studies by Bosson et al. (2014) and Denzler et al. (2014) have empirically assessed the ceRNA hypothesis by quantifying the number MREs that must be added to detect ceRNA-mediated gene regulation. Both studies agree that determining the number of transcriptomic miRNA-binding sites is crucial for evaluating the potential for ceRNA regulation and that miRNA binding sites are generally higher than the number of miRNA molecules. However, they differ in two aspects: (1) the experimental approaches used to determine the number of effective transcriptomic miRNA-binding sites and (2) the impact miRNA concentrations have on the number of binding sites that must be added to detect target gene derepression. The discrepancies between these studies lead to different conclusions with respect to the likelihood of observing ceRNA effects in natural settings, with Bosson et al. observing a ceRNA effect at physiologically plausible and Denzler et al. at unphysiological competitor levels.