Gene expression is a highly complex process that takes place in every cell. Genes, which are small sections of DNA, code for proteins that are vital for the cell’s function and structure. After decades of researching gene expression, we now have a relatively clear picture of what’s going on. But, do we have the full picture yet? Nope. Scientists still continue to unravel some of the underlying mechanisms that control and regulate gene expression. MicroRNAs (abbreviated miRNA), discovered in 1993, brought on a whole new understanding of intricate gene regulatory mechanisms and opened up a Pandora’s Box of possibilities and applications.

What Are MicroRNAs?

MicroRNAs are short (only 22 nucleotides long), highly conserved non-coding RNA molecules that provide a fascinating view into gene regulation. One intriguing aspect of microRNAs is their ability to target and silence the production of proteins that contain a specific sequence that complements their own. Modification in this sequence may result in remarkable changes in gene expression that will of course translate into biological consequences. Here, I provide a review on the latest developments in gene regulation by microRNA sequence editing.

How Next-Generation Sequencing Helped Illuminate MicroRNA Editing

In the past decade, next-generation sequencing data helped illuminate a layer of microRNA regulation through a discrepancy in the microRNA genomic DNA sequence, and the transcribed RNA sequence. When the sequence inconsistency results in a base-conversion from adenosine (A) to inosine (I), (A→I editing), it is regarded as a conversion reaction that is mediated by the activity of the enzymes adenosine deaminase acting on RNA (ADARs).

To conceptually grasp the power of this editing reaction on microRNA activity, it is important to keep these key features in mind:

– Only a mature microRNA commonly functions as a gene silencer.
– A mature microRNA is the final product of two consecutive cuts of the primary transcript by the ribonucleases Drosha and Dicer.
– A→I sequence editing may be lost during the microRNA shortening process unless the modified sequence is present in the mature microRNA sequence.

Editing Within the Mature MicroRNA Sequence: Reassignment of MicroRNA Targets by Recoding

A mature microRNA is about 22 nucleotides long, and within it, the target recognition/“seed” sequence (nucleotide positions 2-8) serves as the microRNA guide in identifying gene targets. Because this sequence defines the microRNA activity, editing in the seed sequence has been termed recoding. This type of gene regulation at the RNA level is a form of temporary gene targeting reassignment. The best-studied example is the microRNA, miR-376, where editing in the seed sequence changes the target specificity of the edited microRNA. A gene target prediction between the edited and non-edited miR-376 yields about 80 unique genes for each with only two overlapping. Furthermore, in vitro and in vivo verification experiments for selected targets confirmed that a single A→I base change in the seed sequence is sufficient to redirect the silencing activity of the microRNA to a new set of targets, and to regulate uric acid levels in a tissue-specific manner.

Editing Outside the Mature MicroRNA Sequence: Alteration in Mature MicroRNA Expression

Although the above mentioned features imply that only the mature edited microRNA may affect gene regulation, studies indicate that editing outside this sequence also has the capacity to regulate gene expression, albeit in a different mechanism.

Studies provide evidence that A→I editing outside the mature microRNA sequence interfere with the mature microRNA processing. Examples were reported in the primary transcripts of miR-142, and miR-151, which displayed resistance to Drosha or Dicer cleaving-activity respectively. Mechanistically, the A→I edits are thought to change the RNA geometry that these enzymes recognize, and thus deregulate their activity. Since the transcript processing is incomplete, the global effect of editing outside the mature sequence is a modification in the expression level of the mature microRNA.

A New Era of Gene Silencers?

MicroRNA editing is a powerful mechanism of gene regulation; it can alter the expression of gene silencers and reassign the targets of gene silencers on a global scale. The later is a fascinating example of gene regulation that allows for an economic and temporary boost in diversity by generating different microRNAs from a pool of identical microRNA transcripts. The applications in medicine are vast and may promote a new era of gene therapy based on microRNA sequence editing.

References:

[1] Y. Kawahara, B. Zinshteyn, T.P. Chendrimada, R. Shiekhattar, K. Nishikura, RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex, EMBO Rep, 8 (2007) 763-769.

[2] Y. Kawahara, B. Zinshteyn, P. Sethupathy, H. Iizasa, A.G. Hatzigeorgiou, K. Nishikura, Redirection of silencing targets by adenosine-to-inosine editing of miRNAs, Science, 315 (2007) 1137-1140.

[3] H. Kume, K. Hino, J. Galipon, K. Ui-Tei, A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency, Nucleic Acids Res, 42 (2014) 10050-10060.

[4] K. Nishikura, Functions and regulation of RNA editing by ADAR deaminases, Annu Rev Biochem, 79 (2010) 321-349.

[5] K. Nishikura, A-to-I editing of coding and non-coding RNAs by ADARs, Nat Rev Mol Cell Biol, 17 (2016) 83-96.

[6] W. Yang, T.P. Chendrimada, Q. Wang, M. Higuchi, P.H. Seeburg, R. Shiekhattar, K. Nishikura, Modulation of microRNA processing and expression through RNA editing by ADAR deaminases, Nat Struct Mol Biol, 13 (2006) 13-21.

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