Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans

Abstract

In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the Caenorhabditis elegans miR-58 miRNA family, composed primarily of the four highly abundant members miR-58.1, miR-80, miR-81, and miR-82, as a model to investigate the redundancy of miRNA family members and their impact on target expression in an in vivo setting. We found that miR-58 family members repress largely overlapping sets of targets in a predominantly additive fashion. Progressive deletions of miR-58 family members lead to cumulative up-regulation of target protein and RNA levels. Phenotypic defects could only be observed in the family quadruple mutant, which also showed the strongest change in target protein levels. Interestingly, although the seed sequences of miR-80 and miR-58.1 differ in a single nucleotide, predicted canonical miR-80 targets were efficiently up-regulated in the mir-58.1 single mutant, indicating functional redundancy of distinct members of this miRNA family. At the aggregate level, target binding leads mainly to mRNA degradation, although we also observed some degree of translational inhibition, particularly in the single miR-58 family mutants. These results provide a framework for understanding how miRNA family members interact to regulate target mRNAs.

sta-1is repressed bymir-58family inCaenorhabditis elegans

“…In particular, we observed a 4.3-fold increment in mixed-stage populations. In close agreement with our results, Subasic et al 10 . have recently analyzed the transcriptome of mir-58f(−) worms at stage L4 and found a 2-fold increase of sta-1 mRNA compared to N2 ( P = 0.002).…”

“…Thus, while single mutants hardly present any phenotypic abnormality, an available mutant lacking 4 miR-58f members (miR-58.1, miR-80, miR-81 and miR-82), mir-58f(−) hereafter, shows remarkable defects in body size, locomotion, and is unable to form dauer larvae 11 . The unaffected mir-58.2 and mir-2209.1 in mir-58f(−) are unlikely to compensate at all for the 4 missing miRNAs in mir-58f(−) , because the expression of mir-58.2 and mir-2209.1 is “essentially undetectable.” 10 In fact, Warf et al. (2011) were unable to fully validated them as miRNAs 12 .…”

Genome-wide identification and characterization of miRNAome from tomato (Solanum lycopersicum) roots and root-knot nematode (Meloidogyne incognita) during susceptible interaction

“…Recently, FLPs ( flp 18 and flp 11) were reported as specific targets of miR-58 in C . elegans [61]. In our study, FLPs were also predicted as targets of miR-58_1 and a significant negative correlation in expression between miR-58_1 and FLP was observed at stages 4 and 5 during susceptible response.…”

miRNAs cooperate in apoptosis regulation during C. elegans development

“…Furthermore, it was proposed that miR-35 and miR-58 family miRNAs cause translational repression of egl-1 mRNA by mediating its deadenylation (Wu et al 2010). Another study reported that the loss of the mir-58 family causes impairment of germline apoptosis; however, a target was not identified (Subasic et al 2015). Therefore, to date, direct regulation of the central apoptotic pathway by miRNAs in vivo has not been demonstrated.…”