miRNA Targeting: Growing beyond the Seed

Abstract

miRNAs are small RNAs that guide Argonaute proteins to specific target mRNAs to repress their translation and stability. Canonically, miRNA targeting is reliant on base pairing of the seed region, nucleotides 2-7, of the miRNA to sites in mRNA 3' untranslated regions. Recently, the 3' half of the miRNA has gained attention for newly appreciated roles in regulating target specificity and regulation. In addition, the extent of pairing to the miRNA 3' end can influence the stability of the miRNA itself. These findings highlight the importance of sequences beyond the seed in controlling the function and existence of miRNAs.

Keywords: miRNA family; miRNA targeting; microRNA; seed pairing.

Figure 1:

Auxiliary pairing of miRNA 3’-end sequences can overcome seed imperfections and confer target specificity to miRNA sisters. A) In C. elegans, the lin-41 3’UTR contains two let-7 miRNA target sites that each feature extensive complementarity to the 3’-half of let-7 and imperfect seed-pairing potential: Site 1 forces a target nt bulge and Site 2 includes an unfavorable G:U base pair (pairing to the miRNA seed, nts 2–7, is shaded gray). While let-7 family members, such as miR-48, can support the same seed-pairing architecture, only let-7 has sufficient 3’-end pairing capacity to regulate lin-41, allowing for normal worm development; loss of lin-41 regulation by let-7 results in lethality (depicted by skull and crossbones) because the let-7 sisters cannot compensate. B) Exchange of the let-7 sites for sequences predicted to correct the seed imperfections but pair more favorably to the 3’-end of miR-48 transfers regulation of lin-41 from let-7 to miR-48. Sites 1’ and 2’ are duplications of a sequence in the dot-1.1 3’UTR that only formed chimeras with miR-48 [19]. C) The inclusion of pairing to nt 8 (shaded yellow) in this context, provides a seed architecture that allows regulation by let-7 or miR-48, regardless of 3’-pairing capacity [22]. Sites 1” and 2” are duplications of the sequence in (B) except for the substitution of U for C to enable canonical pairing to the G at the 8^th position in let-7 and miR-48.

Figure 2:

The structure and position of miRNA-target interactions impose different regulatory outcomes. Canonical miRNA target sites reside in 3’UTRs, require seed-pairing, and rely on the AGO co-factor GW182/ TNRC6 to recruit deadenylases and other factors that act to destabilize and repress translation initiation of the target mRNA (top) [4,7]. The example is a 3’UTR site engineered to limit pairing to the miR-20a seed region [31]. A new class of target sites are located in coding sequences (CDSs), lack seed complementarity and, instead, offer extensive pairing to miRNA 3’-ends; these types of sites seem to block translation elongation independently of GW182/ TNRC6, resulting in reduced protein but not mRNA levels of the target (bottom) [31]. The example is the CDS site in exon 2 of DAPK3 mRNA paired to miR-20a [31].

Figure 3:

Extensive pairing between a miRNA and target can induce Target-Directed miRNA Degradation (TDMD). TDMD of miR-29b can be triggered by pairing to a conserved region in the zebrafish lncRNA, libra, or the mouse Nrep 3’UTR (top) [40]. A site in the 3’UTR of Serpine1 induces TDMD of miR-30b/c in mouse fibroblasts (bottom left) [42]. In mice, pairing of miR-7 to a site in the lncRNA Cyrano results in rapid decay of the miRNA through TDMD [41].