Research Article

A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming

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Science  18 Dec 2020:
Vol. 370, Issue 6523, eabc9546
DOI: 10.1126/science.abc9546

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Turning the tables on microRNA decay

MicroRNAs help to regulate many genes in animal cells. Each microRNA associates with an Argonaute (AGO) protein, forming a complex in which the microRNA pairs with a messenger RNA (mRNA) target and AGO recruits factors that accelerate mRNA decay. However, for some unusual targets, the reverse occurs: Pairing to the target recruits factors that accelerate microRNA decay rather than degradation of the mRNA. Working independently, Shi et al. and Han et al. elucidate the mechanism of this phenomenon. They found that pairing to the unusual targets recruits a ubiquitin ligase that causes degradation of AGO, thereby exposing the microRNA to cellular nucleases. Mutating the ubiquitin ligase in diverse animals and cell types deregulates numerous microRNAs, implying that this phenomenon is widely deployed to sculpt microRNA levels.

Science, this issue p. eabc9359, p. eabc9546

Structured Abstract

INTRODUCTION

MicroRNAs (miRNAs) are a class of highly conserved small regulatory RNAs. After loading into Argonaute (AGO) proteins, miRNAs promote the degradation and reduced translation of the target mRNAs to which they bind. Consistent with the essential functions of miRNAs in development and physiology, elaborate mechanisms that control miRNA transcription and biogenesis have been uncovered. However, much less is known about the mechanisms that control miRNA turnover. Although miRNAs are generally very stable, with half-lives extending to days, some miRNAs are rapidly degraded. Thus, regulated miRNA decay mechanisms exist. Perhaps the most well-characterized pathway for miRNA turnover is a process called target-directed miRNA degradation (TDMD), which occurs when a miRNA engages a target with extensive complementarity. Unlike canonical targets, TDMD-inducing targets typically exhibit extended base pairing with the miRNA 3′ end. Multiple classes of targets that trigger TDMD have been identified, including synthetic transgenes, virally encoded transcripts, and endogenous protein-coding and noncoding RNAs. Nevertheless, the mechanism that leads to miRNA degradation when a TDMD target is encountered is poorly understood.

RATIONALE

Nontemplated nucleotide addition and removal at the miRNA 3′ end occurs when a miRNA engages a TDMD target. This process, called tailing and trimming, has been proposed to be an essential step in the decay mechanism. However, depletion of terminal nucleotidyltransferases or nucleases that participate in tailing and trimming does not stabilize miRNAs undergoing TDMD. Thus, the role of tailing and trimming in this pathway remains unclear. Furthermore, trans-factors that are required for TDMD have yet to be identified. We performed a genome-wide CRISPR-Cas9 screen to investigate this important mechanism of miRNA regulation and to address these unresolved questions.

RESULTS

The highly conserved long noncoding RNA CYRANO triggers robust TDMD of miR-7 in the human cell line K562. An enhanced green fluorescent protein (EGFP) reporter transcript was designed to monitor decay of miR-7 in this system and used in a genome-wide CRISPR-Cas9 screen to identify factors that are required for TDMD. The screen revealed that TDMD is mediated by a cullin-RING ubiquitin ligase (CRL) complex containing the substrate adaptor ZSWIM8, as well as core CRL components elongins B and C (ELOB and ELOC), cullin 3 (CUL3), ARIH1, and RBX1. The ZSWIM8 ubiquitin ligase was required for TDMD induced by multiple transcripts in multiple cell lines. miRNA turnover mediated by the ZSWIM8 complex did not require tailing and trimming. Instead, ubiquitin transfer activity and activity of the proteasome was required for miRNA degradation directed by this complex. Moreover, the ZSWIM8 CRL interacted with AGO proteins. Conserved surface-exposed lysine residues on AGO2, particularly K493, were required for TDMD. These data suggest a role for direct ubiquitylation of AGO in this miRNA decay pathway. Small RNA sequencing in diverse cell lines after depletion of ZSWIM8 revealed stabilization of many miRNAs not previously known to be regulated by TDMD.

CONCLUSION

Base pairing of a miRNA with a TDMD-inducing transcript promotes broad structural rearrangements of AGO. Our findings suggest a model in which the ZSWIM8 ubiquitin ligase recognizes this TDMD-associated conformation, resulting in ubiquitylation and subsequent proteasomal decay of the miRNA-containing complex. This likely leads to concomitant release and degradation of the miRNA by cytoplasmic RNases. Our analyses of miRNA expression in ZSWIM8-deficient cells, coupled with the strong evolutionary conservation of ZSWIM8 and its associated CRL components, suggest that this pathway may act broadly to regulate miRNA expression in metazoan development and physiology. miRNAs in plants, and other classes of small RNAs such as piwi-interacting RNAs, are naturally 2′-O-methylated at their 3′ ends. This modification prevents tailing and trimming. The ability of the ZSWIM8 complex to carry out TDMD in a tailing and trimming–independent manner raises the possibility that these small RNAs may also be regulated by a TDMD-like mechanism involving proteasome-dependent turnover.

The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation.

Canonical miRNA-mediated silencing, primarily involving base pairing of the miRNA seed sequence, results in target repression and recycling of the AGO–miRNA complex. In contrast, extensive miRNA–target complementarity can trigger recognition by the ZSWIM8 ubiquitin ligase, resulting in proteasomal turnover of the miRNA-containing complex and miRNA decay, with release of the target for additional rounds of TDMD. m7G, 7-methylguanosine; An, polyadenosine tail; E2, ubiquitin-conjugating enzyme; Ub, ubiquitin.

Abstract

MicroRNAs (miRNAs) act in concert with Argonaute (AGO) proteins to repress target messenger RNAs. After AGO loading, miRNAs generally exhibit slow turnover. An important exception occurs when miRNAs encounter highly complementary targets, which can trigger a process called target-directed miRNA degradation (TDMD). During TDMD, miRNAs undergo tailing and trimming, suggesting that this is an important step in the decay mechanism. We identified a cullin-RING ubiquitin ligase (CRL), containing the substrate adaptor ZSWIM8, that mediates TDMD. The ZSWIM8 CRL interacts with AGO proteins, promotes TDMD in a tailing and trimming–independent manner, and regulates miRNA expression in multiple cell types. These findings suggest a model in which the ZSWIM8 ubiquitin ligase mediates TDMD by directing proteasomal decay of miRNA-containing complexes engaged with highly complementary targets.

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