Recent advances in understanding microRNA function and regulation in C. elegans

Abstract

MicroRNAs (miRNAs) were first discovered in C. elegans as essential post-transcriptional regulators of gene expression. Since their initial discovery, miRNAs have been implicated in numerous areas of physiology and disease in all animals examined. In recent years, the C. elegans model continues to contribute important advances to all areas of miRNA research. Technological advances in tissue-specific miRNA profiling and genome editing have driven breakthroughs in understanding biological functions of miRNAs, mechanism of miRNA action, and regulation of miRNAs. In this review, we highlight these new C. elegans findings from the past five to seven years.

Keywords: Aging; Argonaute; C. elegans; Circadian rhythm; Development; MiRNA; Post-transcriptional gene regulation; RISC; Stress; TDMD; Target-directed microRNA degradation; Tissue-specificity.

Figure 1.. Approaches to miRNA target identification and validation facilitated by CRISPR.

(A) Wild type miRNA function and phenotype. (B) miRNA mutant displaying corresponding phenotype. (C) Mutation of miRNA binding site in phenotype-relevant target phenocopies miRNA mutant. (D) Compensatory mutations in miRNA that restore binding to mutant binding site rescue phenotype in (C). (E) Precise mutations can dissect contributions of individual nucleotides to the miRNA-target interaction. (F) Binding site mutation and phenotypic readout can be multiplexed; using phenotypic selection coupled with deep sequencing of mutated sites further leverages labor-saving advantages of a multiplexed approach.

Figure 2.. RISC co-factors drive mechanism of target repression.

A unique RISC in the embryo and germline appears to act independently of AIN-1/2. This RISC localizes transcripts to P granules through interactions with GLH-1, and these miRNA targets are stabilized and held translationally repressed. A direct interaction between GYF-1 and the embryonic/germline RISC has not yet been observed; however, GYF-1 is required for the functions of the embryonic mir-35 family, suggesting it is a component of the embryonic/germline RISC. In somatic tissues, AIN-1 is required for the function of many miRNAs such as lin-4, let-7 and lsy-6. AIN-1 mediates miRNA function through deadenylation/decay of targets by recruiting NTL-1 and interacting with PAB-1. ALG-1 and AIN-1 both interact with P-body localizing proteins CGH-1 and NHL-2.

Figure 3.. MiRNA decay mechanisms.

Both miRNAs and Argonaute proteins are stabilized by interacting with each other. TEG-1 associates with and stabilizes RISC. Decay of many miRNAs is driven by XRN-1, XRN-2, DCS-1, and PQN-59. The factors driving these non-specific miRNA decay mechanisms are not fully known. In mammals, TDMD is a well-characterized sequence-specific decay mechanism in which base pairing in the seed sequence, coupled with extensive complementarity at the miRNA 3′ end, leads to the recruitment of the ubiquitin ligase ZSWIM8, resulting in the degradation of the RISC. Similarly, in C. elegans the decay of mir-35 is dependent on the ZSWIM8 ortholog EBAX-1, and the seed sequence of mir-35, but independent of the miRNA 3′ end sequence. In TMMP, the availability of a miRNA target leads to stabilization of the miRNA; the mechanism is currently unknown.