MicroRNAs: From Mechanism to Organism

1Regulation of gene expression by small RNAs emerged as an ancient feature of cellular biology and is found in all three domains of life (bacteria, archaea and eukarya). Having evolved primarily as a means of defense against foreign nucleic acids the principle of small RNAs specifically guiding effector proteins to selected nucleic acids via antisense-complementarity is a recurrent theme in biology. At their core, these RNA-based interference (RNAi) systems consist of two components, a nucleic acid allowing for sequence-specific target recognition, and an effector protein that mediates downstream effects with varying outcomes.

2In eukaryotes, the effector proteins that mediate the silencing of target nucleic acids are part of the Argonaute protein family. After their origin in prokaryotes, Argonautes diversified into a versatile class of effector proteins, forming the core of various multiprotein regulatory systems or RNA-Induced Silencing Complexes (RISC). They all share common structural elements and the ability to bind short, single stranded RNAs in a conformation that enables base pairing with target RNAs. The other critical protein component of eukaryotic RNA-induced silencing pathways are nucleases that process precursor RNAs into small RNAs that can be loaded onto Argonaut proteins. A major player in multiple RNAi pathways is Dicer, an RNAse III type endonuclease that cleaves double-stranded RNA molecules to generate targeting-competent small RNAs that guide the effector machinery. Although no prokaryotic homolog of Dicer has been found to date, the origins of individual domains can be traced back to prokaryotes. Together, RNase III type endonucleases and Argonaute proteins lie at the heart of diverse small RNA based pathways involved in multifaceted aspects of molecular biology.

3The different modules that constitute the eukaryotic RNAi systems likely originated in archaea, bacteria, and bacteriophages. This core structure has diversified, specialized, and acquired new functions in the course of eukaryotic evolution. A key innovation in diverse lineages was the ability to not only load and target foreign or parasitic RNAs, but also to feed endogenously produced RNAs into the existing RNAi pathways to achieve gene regulation. This formed the basis for the emergence and expansion of the endogenous class of small RNAs called microRNAs (miRNAs), whose regulatory potential has been harnessed in animals, plants, and other eukaryotic lineages for the establishment of elaborate gene regulatory networks that control development and physiology (Figure 1).

4The complexity of multicellular organisms relies on the segregation of functions across many distinct cell types, which requires intricate gene regulatory mechanisms. As versatile repressors of gene expression, miRNAs are thought to facilitate the generation of different cell types with highly specialized physiology. It comes as no surprise that the evolution of multicellular organisms has been accompanied by an increase in complexity of the miRNA pathway and the miRNA repertoires. The use of this increased diversity of repressors has been exploited by the addition of multiple mechanisms that control which miRNAs are produced at specific times and in specific cell types; at what levels these accumulate to act effectively; and what the molecular consequences of their repression are.

5A comprehensive understanding of the contributions of miRNAs thus requires bridging biochemical and mechanistic insights with the organismal level. When and where does miRNA-mediated regulation take place? How is the production of a specific miRNA controlled in space and time to achieve that? And how do miRNAs integrate into cellular gene regulatory networks that control development and physiology? Recent technological advances have enabled more quantitative assessment of the kinetics of miRNA production and turnover, and context-dependent differences in composition of miRISC during distinct developmental stages. This allows a more nuanced view of when, where and how miRNAs are utilized within animal development and post-developmental processes. Moreover, the sequencing of an increasing number of genomes has upgraded our ability to place miRNAs and the associated protein machinery into an evolutionary context. These layers of understanding will lead us to broader concepts of what miRNAs contribute to the phenotypic complexity observed in present-day organisms.

6We do not attempt to provide a comprehensive survey of all the miRNAs that have been studied and their functions in different animals, for which we suggest the following starting points. Instead, we emphasize general concepts from diverse mechanistic studies to understand how multicellular organisms have exploited the potential of this broad class of repressors. We first focus on how miRNA biogenesis is controlled and discuss how the different modes of regulation can affect miRNA function within an animal. Next, we discuss how different composition of the RISC complex and different cellular contexts can result in distinct outcomes of miRNA-mediated repression. Finally, we present an updated overview of how the miRNA repertoire has evolved and what this teaches us so far about how miRNAs have acquired functionality during evolution.

7In 1993, the product of the Caenorhabditis elegans gene lin-4 was surprisingly found to give rise to a small non-coding RNA, processed from a longer hairpin precursor, which functions by repressing protein production from the lin-14 mRNA via an antisense RNA–RNA interaction. First thought of as a nematode peculiarity, it became clear in the early 2000s that such endogenous small RNAs like lin-4, in particular let-7, play a fundamental role across eukaryotic lineages. The discovery of lin-4 and let-7, followed by the identification of hundreds of endogenous small RNAs derived from hairpin precursors in animal genomes, laid foundation to the miRNA field. Not only is the protein machinery associated with miRNAs highly conserved, but so are many miRNAs – with >30 miRNAs shared across all bilaterian animals, and hundreds of others conserved within specific clades. Moreover, at least 37% of Drosophila and 60% of human protein-coding transcripts are subjected to selective pressure to retain miRNA binding sites, underscoring the biological significance of miRNA-mediated gene silencing.

8miRNAs are 21–23 nt small RNAs that elicit post-transcriptional downregulation of protein output from their target mRNAs. This is typically achieved through a combination of translational inhibition and promotion of mRNA decay. The origin of miRNA-biology lies in the evolution of a mechanism that allowed for processing of long endogenous transcripts into short RNA duplexes that are further recognized and cleaved by Dicer. In animals this is achieved by the Microprocessor complex, composed of the RNase III endonuclease Drosha and its co-factor Pasha (Partner of Drosha, or DGCR8 in vertebrates). Cleavage of a primary miRNA transcript by the Microprocessor in the nucleus releases a hairpin precursor, that upon export to the cytoplasm is further cleaved by Dicer to give rise to a short RNA duplex with characteristic 2-nt 3′ overhangs. From this duplex, one strand is preferentially loaded into an Argonaute protein to generate a functional miRNA-induced silencing complex (miRISC) (Figure 2).

9Drosha and Pasha/DGCR8 originated in unicellular holozoans after fungi branched from the pre-metazoan lineage, placing the appearance of miRNAs before the onset of multicellularity. However, plants do not encode a homolog of Drosha or Pasha but process primary miRNA transcripts via the Dicer-homolog DCL1 (Dicer like 1), which generates mature miRNAs according to a similar principle involving two sequential endonucleolytic cleavage events. This led to the initial hypothesis that miRNAs evolved independently in animals and land plants. However, the possibility that the last common ancestor of these lineages might have already employed a common miRNA-like pathway for post-transcriptional regulation is not to be dismissed. Nevertheless, after their introduction, the number of miRNAs continuously expanded during the course of evolution, providing multicellular organisms with a diversified toolset for regulation of gene expression.

10Regulation by miRNAs evolved into a key feature of multicellular organisms. As general repressors of gene expression, miRNAs have been incorporated into gene regulatory networks that control diverse developmental and post-developmental processes. No higher metazoan lineage has tolerated the loss of essential miRNA pathway components. In fact, defects in the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied.

11In C. elegans, removal of the miRNA-specific Argonautes alg-1 and alg-2 causes embryonic lethality with a predominant arrest in the morphogenetic process of elongation. Disruption of ago1 in Drosophila causes embryonic lethality with notable nervous system abnormalities. Loss of Dicer in Zebrafish results in abnormal gastrulation causing severe defects in brain development and organogenesis. Notably, injection of a miR-430 duplex into embryos considerably rescued neuronal defects, indicating an outstanding role of a single miRNA in early fish development. Mouse embryos lacking Dicer1 or Ago2 fail to undergo gastrulation, accompanied by a malformation of germ layers. Moreover, this phenotype is recapitulated in animals bearing a deletion of Dgcr8. In plants, disruption of DICER-LIKE1 leads to embryonic arrest early in development, likely caused by a failure to prevent precocious differentiation events. Interpretation of these experiments should consider possible miRNA-independent functions of disrupted miRNA-pathway factors, as such roles have been demonstrated for Drosha, Pasha and Dicer. However, given that removal of different components in the miRNA-pathway causes highly similar phenotypes, it is strongly suggested that miRNA-deficiency underlies the observed defects.

12Whereas miRNAs are collectively essential in animals, uncovering the functions of many individual miRNAs has been challenging. This is in part due to redundancy, most notably among miRNAs that fall into so-called families and share targeting specificity, but also redundancy with other repressive mechanisms that contribute to the output of gene regulatory networks (acting either at the RNA or protein levels). For example, in Drosophila, the near-complete loss of miRNA-mediated repression is tolerated to a large extent if general metabolism is simultaneously slowed down. This suggests that under conditions of slow developmental tempo, the timely downregulation of targets or the establishment of the right protein levels, to which miRNAs contribute, might be achieved through compensatory mechanisms. In a number of cases, the contribution of miRNAs has been revealed only in sensitized genetic backgrounds or upon environmental perturbation, such as exposure to extreme temperatures or pathogen stress. This suggests that the activity of some miRNAs is redundant with other factors that are influenced by environmental conditions. It is also likely that the function of many miRNAs has not been uncovered, even if they play non-redundant roles, because they are often expressed with very high spatial and temporal specificity and may function predominantly in specialized cell types within complex multicellular organisms.

13Multicellular organisms have taken advantage of the potential of miRNA-mediated regulation employing multiple mechanisms to control the production of miRNAs in distinct cell-types, under varying conditions, or during different developmental stages. miRNA biogenesis begins with transcription of a primary transcript by RNA polymerase II (Figure 2). Transcriptional regulation will thus determine whether a miRNA will be produced in the first place, and in general miRNA abundance correlates well with the rates of primary-miRNA transcription. At the organismal level, there is evidence that for most miRNAs, transcriptional control is the main determinant of cell-type specificity. However, the maturation of primary miRNAs, initially by the Microprocessor in the nucleus and later by Dicer in the cytoplasm (Figure 2), can also be regulated, contributing significantly to the dynamics of accumulation and steady-state abundance of different miRNAs. Moreover, it became evident that regulation of miRNA decay plays an important role in determining the functional levels of individual miRNAs.

14Transcription of each pri-miRNA is under the control of specific transcription factors and enhancers that outline their expression patterns. For example, an elaborate transcriptional mechanism determines the expression of the miRNA lsy-6 in a single neuron in C. elegans. In contrast, post-transcriptional regulation of miRNA biogenesis is achieved at two different levels: (i) globally, by controlling the shared core machinery that produces most miRNAs, e.g., modulating levels or activity of the Microprocessor, and (ii) at the level of individual miRNAs, exploiting unique sequence and structural features of diverse miRNA precursors which impact interaction with the biogenesis machinery. Such interactions are often facilitated by various RNA binding proteins (RBPs).

15Recent advances in the use of metabolic labeling of RNA have enabled kinetic studies of different steps during the life of a miRNA, and provided insight into how the rates of these steps vary for distinct miRNAs. An in-depth analysis in Drosophila S2 cells revealed that the rates of mature miRNA biogenesis range from 17 to >200 molecules/minute/cell. However, the loading into Argonaute is significantly slower and in fact represents a kinetic bottleneck in the production of functional miRISC. As a consequence, a large fraction of the miRNA duplexes produced by Dicer (approximately 40%) is degraded before loading. Other reports found only <10% of cellular miRNAs are bound by Argonaute. This seemingly wasteful strategy ensures specific loading of Argonaute with miRNAs, which compete against other abundant duplex RNAs originating from tRNAs, rRNAs, snRNAs, or snoRNAs. Consistently, Argonaute binding is a better indicator of the inhibitory potential of a miRNA than its overall concentration. For this specificity mechanism to be effective, Argonaute levels need to be limited. This is achieved in large part through the relatively short half-life of empty Argonaute, which is efficiently ubiquitinated and degraded.

16Another important contributor to miRNA abundance is their stability. While overall miRNAs are among the most stable cellular RNAs, individual species can range in stability from minutes to more than a day. Rates of decay can be modulated by external stimuli to remodel the miRNome, as is the case for light-regulated retinal miRNAs. In general, neuronal miRNAs in mammals appear to have a high turnover rate compared to other cell types, and their abundance can be rapidly regulated in connection with neuronal activity. Together with the biogenesis rates, the different decay rates determine the steady-state abundance of miRNAs, such that two miRNAs can reach the same abundance through contrasting strategies: a miRNA with slow biogenesis and slow decay can accumulate to the same concentration as one with fast biogenesis and fast decay. The first case will result in a stable concentration that is less likely to change upon small perturbations, while the second is energetically more costly but provides potential for dynamic regulation. Such different strategies for accumulation have important consequences for miRNA function, and further investigation of how these different rates come about will provide critical insight. Nevertheless, this quantitative understanding already provides a framework for determining the ability of miRNAs to reach the necessary cellular concentrations to execute their repressive functions.

17Effective repression by miRISC requires a high concentration of a miRNA relative to its target. To achieve this, synthesis of a number of miRNAs begins long before the onset of their repressive function. For example, the miRNA lsy-6 in C. elegans, which functions in a sensory neuron by repressing the transcription factor COG-1, is produced in the mother of the sensory neuron. Transcription of cog-1 begins in the postmitotic neuron several hours later in a cell that has high concentration of lsy-6. This likely contributes to the ability of lsy-6 to act as a genetic switch by completely preventing COG-1 expression. Another example of this is the essential C. elegans miRNA let-7, which is required for transition of the last larval stage to adulthood, yet starts being transcribed in the first larval stage. Taking into account the relative dynamics of accumulation of a given miRNA and its target/s offers helpful insight for understanding the contribution of that miRNA to specific cellular processes.

18These are the general forces that determine whether a miRNA is made and if so, to what level it accumulates relative to its targets. The core mechanisms that control each of these steps have been studied in great detail in different cell-based systems. Multicellular organisms take advantage of various ways to adjust these mechanisms to generate the necessary spatio-temporal specificity and the dynamics of miRNA expression that support development and homeostasis.

19Processing of primary-miRNA transcripts (pri-miRNAs) initiates co-transcriptionally. In Drosophila, Pasha/DGCR8 can associate directly with RNA pol II via its phosphorylated C-terminal domain, linking transcription with the first step of miRNA maturation. Interaction of DGCR8 and Drosha with pri-miRNAs occurs via recognition of a hairpin secondary structure flanked by single-stranded RNA and leads to cleavage by Drosha to release a precursor hairpin. The efficiency and the accuracy of this reaction are crucial determinants of miRNA abundance and targeting specificity, respectively. Because miRNAs bind their targets primarily through nucleotides 2–8 relative to the 5′ end of the miRNA (the “seed” sequence), a change in cleavage site that affects the 5′ end of a miRNA even by a single nucleotide can drastically alter target specificity of that miRNA. The choice of cleavage site by Drosha is crucial for setting the 5′ end of both miRNA arms: the 5p arm directly and the 3p indirectly by determining the register for the subsequent cleavage by Dicer. Interestingly, recent mapping of Drosha cleavage sites with single nucleotide resolution in human cell lines (HEK293T and HeLa cells), revealed that some miRNAs undergo alternative processing resulting in different 5′ and 3′ ends. This has the potential to further diversify the miRNA-repertoire.

20Once a pri-miRNA is processed to a precursor hairpin (pre-miRNA) in the nucleus, it will be exported and further cleaved in the cytoplasm by Dicer. Consistent with its evolutionary origin before the appearance of miRNAs, Dicer has a wider range of substrates than the Microprocessor – it can cleave RNA duplexes of any length, as long as they have a 2-nt 3′ overhang (and in some cases even blunt-ended duplex RNA). The domain structure of Dicer serves as a molecular “ruler,” such that the two RNAse III active sites are positioned at a defined length from the 3′ overhang of the pre-miRNA and determine the length of the mature small RNA. Dicer cooperates with other RNA binding proteins, PACT or TRBP in humans, and Loquacious in Drosophila. This interaction can affect not only the efficiency of the processing, but also the length of the mature miRNA produced. Therefore, together with Drosha, Dicer defines not only the abundance but also the ends of the mature miRNAs that will be loaded into Argonaute.

21Because of its broader activity, Dicer processes not only pre-miRNAs, but also different endogenous and foreign duplex RNAs to produce other classes of short interfering RNAs (siRNAs). Whereas Drosophila has two different Dicer proteins, one specialized for miRNA (Dcr-1) and the other for siRNA biogenesis (Dcr-2), many other animals have a single type of Dicer. The involvement of this enzyme in two different pathways creates a bottleneck that in some animals leads to competition between the two different types of small RNA precursors. In C. elegans for example, downregulation of the endo-siRNA pathway results in an increase of miRNA-biogenesis, whereas induction of exogenous RNAi competes with both endo siRNA and miRNA production. This suggests that, at least in some contexts, Dicer can be limiting for small RNA production.

22Processing by the Microprocessor and by Dicer is subjected to diverse regulatory mechanisms. These can either affect Drosha and DGCR8 or Dicer themselves to broadly impact the biogenesis of multiple miRNAs, or specifically regulate the maturation of individual miRNAs, typically through the action of RNA binding proteins (RBPs) that recognize unique features of primary and precursor miRNAs.

23Pri-miRNAs share some broad structural features, but they can differ substantially in the length of their stems, the sequences in their loops, and the sequences flanking the hairpin, posing a challenge for efficient and specific processing by the Microprocessor. Indeed, not all wild-type pri-miRNAs are optimal targets for Drosha or DGCR8 binding, resulting in a broad range of processing efficiencies, and different degrees of sensitivity to the presence of co-factors like for example DGCR8’s co-factor, the iron-containing porphyrin heme. A number of sequence motifs that increase the specificity and efficiency of processing by the Microprocessor have been identified; for instance, apical elements in the hairpin, most prominently a UGU motif and the mGHG-motif on the basal side, which seems to be a key determinant of cleavage site selection in many pri-miRNAs. Highlighting the importance of the pri-miRNA sequence and structure for its correct processing, a single nucleotide change in the apical loop of pri-mir-30c-1 found in some patients with breast and gastric cancer results in increased processing and thus higher miR-30c-1 abundance. This was attributed to enhanced binding of SRSF3, a protein of the SR family that promotes Microprocessor cleavage.

24The diversity in pri- and pre-miRNA sequences means that different steps might be rate-limiting for individual precursors, and this has enabled the evolution of additional regulatory mechanisms. A number of individual miRNAs are subjected to unique modes of regulation via specific interactions with different RNA-binding proteins (RBPs). A recent mass spectrometry-based screen using various human cell line lysates identified numerous RBPs that impact processing of subsets of miRNA-precursors and ultimately the expression of target mRNAs. The binding specificity of many of these seems to be determined by the terminal loop, in which the RNA is single-stranded and typically exposed for contact with other proteins. However, interestingly a few RBPs also bind the stem of specific miRNA hairpins. A complementary in silico approach using published eCLIP-data has also identified a number of novel RBP:pre-miRNA interactions affecting processing of specific miRNAs.

25Some RBPs have been shown to recruit terminal nucleotidyl transferases, most commonly uridyl transferases or TUTases. Post-transcriptional modifications of precursor or mature miRNAs can impact the kinetics of biogenesis or silencing. Uridylation of mature miRNAs by TUTases tends to promote decay. However, uridylation of pre-miRNAs may either promote decay or have stabilizing effects and affect further processing by Dicer, depending on the 3′ end structure of the precursor. Terminal miRNA modification by TUTases occur in Bilateria as well as in more basal animal clades such as Cnidaria and Porifera. In fact, TUTases acting on small RNAs were already present in the last common ancestor of all animals, underscoring the fundamental involvement of these mechanisms in miRNA biology.

26The general activities of Dicer and the Microprocessor can also be regulated, with global consequences for miRNA output. A common regulatory mechanism is through post-translational modifications of the enzymes themselves, or their cofactors. Regulation of Dicer activity for example is affected by phosphorylation of its binding partner TRBP, resulting in increased stability of the Dicer-TRBP complex and enhanced pre-miRNA processing activity. Dicer itself can be phosphorylated on two conserved residues, resulting in its nuclear translocation and inhibition in worms, mice and humans. This inhibitory mechanism has been implicated in the reduction of mature miRNA levels in the C. elegans germline, contributing to precise gene expression changes in the oocyte-to-embryo transition. In general, post-translational modifications may serve to integrate diverse cellular signaling pathways with the production of miRNAs.

27Moreover, levels of the processing machinery can vary across different cell types or under different conditions, also impacting the global miRNA output. A survey of Drosha expression levels across different mouse tissues revealed differences in the range of 4–10-fold, with the brain having the highest and the liver the lowest level of Drosha mRNA and protein. Lower Drosha expression enhances the inherent differences in processing efficiency of different pri-miRNAs, resulting in the deregulation of subsets of miRNAs with specific properties. The contribution of some of these mechanisms to the development and physiology of animals remains to be tested. Nevertheless, the dysregulation of the miRNA biogenesis machinery has been associated with diverse forms of cancer, typically resulting in a global repression of miRNA maturation.

28The final step for producing a functional miRISC is the loading of a miRNA into Argonaute. This seems to be the rate-limiting step in a number of contexts, likely related to the fact that loading does not simply reflect binding of an RNA to Argonaute, but follows a number of steps that require assistance from other factors, including chaperones and energy from ATP. As with every other step of miRNA biogenesis, miRNA loading can also be affected by specific features of the miRNA duplex, such as presence of a 5′ phosphate, identity of the 5′ terminal nucleotide and stability of the duplex. These features also determine which of the two duplex strands is preferentially loaded on Argonaute and acts as a mature miRNA; the opposite strand, or miRNA∗, is typically rapidly degraded. In addition, specific RNA binding proteins that impact the loading on Argonaute either positively or negatively have been described. For example, TDP43 disrupts loading of miR-1 and miR-206, two muscle-specific miRNAs, while hnRNPD0 supports loading of let-7b.

29The effects of all these regulatory mechanisms at the organismal level can in principle have two different types of consequences. On the one hand, post-transcriptional regulation of miRNA biogenesis may be used to encode temporal or spatial information in a developing animal. Such is the case of LIN28, which acts as a conserved post-transcriptional repressor of let-7-family miRNA biogenesis. LIN28 recruits TUTases that ultimately prevent Dicer-recognition and promote decay via the exonuclease Dis3L2. Release of LIN28-mediated repression of let-7 maturation provides a temporal switch in different contexts during progression of animal development.

30However, most of the RBPs that affect biogenesis and loading are ubiquitously or very broadly expressed, suggesting that they may rather contribute to achieving homeostatic levels of specific miRNAs. This could be necessary to compensate for individual miRNA features that make them better or worse substrates of the biogenesis machinery. It is also possible that some of these RBPs have different expression levels or modifications in different tissues that might directly contribute to the spatio-temporal specificity of miRNA production. Another possibility is that some regulators are used to restrict the production of miRNAs to specific sub-cellular localizations. An extreme example of this is the synapse-specific maturation of miRNAs by Dicer upon neuronal activation.

31The ancestral mechanism of small RNA guided effector proteins involves irreversible destruction of targeted nucleic acids by cleavage. This miRNA mode of action, which is usually accompanied by near-perfect target complementarity, is prevalent in plants and also observed in basal metazoan lineages like Cnidaria. Bilaterian animals on the other hand, predominantly employ a mechanism that relies on partial base pairing between the “seed” region of a miRNA (nucleotides 2–8) and sequences typically in the 3′ UTR of mRNAs. Recruitment of miRISC in bilaterians usually results in the downregulation of protein output through a combination of translation inhibition and target mRNA decay (;; Figure 3).

32Appearance of the slicing-independent, seed-based mechanism laid the foundation for functional diversification of miRNA biology in animals. Compared to a mode of target recognition that involves full sequence complementarity, a mechanism that requires only partial base-pairing has the potential to greatly increase the target repertoire of any miRNA. This likely expanded the overall potential of miRNA-mediated repression in bilaterian animals, enhancing the connectivity of gene regulatory networks, and contributing to cell-type diversification and acquisition of morphological complexity during evolution.

33The best understood mechanism of miRNA-mediated repression in animals relies on a protein of the GW182 family, which together with Argonaute forms the core of what is considered the canonical miRISC. Members of the GW182 protein family (e.g., GW182 in Drosophila, AIN-1/2 in C. elegans and TNRC6 in humans) are rapidly evolving but share Gly-Trp repeats that bind to conserved pockets in Argonaute proteins. Through other domains, GW182 proteins recruit RNA-processing factors, repressing translation as well as enhancing mRNA turnover. The precise mechanism for translational repression remains to be resolved; however, the emerging consensus is that it involves inhibition of cap-dependent translation initiation via interaction with eIF4F. GW182 proteins also recruit the PAN2-PAN3 and CCR4-NOT deadenylase complexes, ultimately triggering mRNA decay (;;;;;;; Figure 3). GW182 has been proposed to promote the formation of phase-separated condensates containing miRISC and target mRNAs, increasing the local concentration of deadenylases and other factors for efficient repression. GW182 is also present in Nematostella, where it is able to interact with Argonaute and the CCR4-NOT complex, suggesting that this mechanism originated in the last common ancestor between Cnidaria and Bilateria. Experimental uncoupling of translational inhibition and mRNA decay has proven challenging, as the two processes are intimately linked. Still, analyses of the dynamics of miRNA-mediated silencing in zebrafish early embryos and in mammalian cells in culture, revealed that miRNAs first repress translation initiation and then induce mRNA decay. The relative contribution of these two mechanisms to biological function remains a matter of debate, but as we discuss below multiple pieces of evidence indicate that this may be determined by the cellular context and miRISC composition.

34Despite the conserved nature of the canonical miRNA targeting mechanism, there is an increasing number of examples highlighting context-dependent variability in the mode and functional consequence of miRISC targeting (Figure 4). This variability can arise from two different mechanistic sources. First, miRISC can have non-canonical composition in different cell types or distinct developmental stages (e.g., differential presence or abundance of GW182 and other proteins that act as facultative Argonaute interactors). In metazoans, such variations are observed most notably between soma and germline, and we expand on this in the next section. Second, as perfect target complementarity is not a prerequisite, there are different possible miRNA:mRNA interaction modes. Whereas the majority of miRNA binding sites are located in the 3′ UTR and involve pairing to the seed region of a miRNA, these features can differ with varying functional consequences; from efficiency of silencing depending on the relative location of miRNA-binding sites within the target mRNAs; to degradation of the miRNA itself, if target pairing extends to the 3′ end of the miRNA.

35The mode of miRNA targeting and the effects that different RISC complexes will exert on their targets vary significantly across different eukaryotic clades. Even within a single animal, the composition and functional consequences of miRISC can differ in specific biological settings. The first evident variation is in the Argonaute component itself, e.g., C. elegans evolved more than 25 Argonaute proteins. ALG-1 and ALG-2 are the main miRNA-related Argonautes. They function redundantly to a large degree, and only loss of both simultaneously causes penetrant embryonic lethality. However, they do display some functional differences which may stem from differences in expression patterns and levels (ALG-2 appears to be dominantly expressed throughout embryogenesis) as well as in miRNA-binding preference. Interestingly, another Argonaute, ALG-5, has recently been implicated in miRNA-mediated silencing in the worm. ALG-5 is expressed in the germline, where it associates effectively with only a subset of miRNAs and plays a role in gametogenesis. Insects such as cockroaches, from a basal clade, also have two partially redundant Argonautes for miRNA mediated silencing. However, subsequent specialization took place in more derived clades like Drosophila, which encodes one Argonaute for siRNA and another one for miRNA-mediated silencing.

36Most of the variation in outcome of miRISC binding to an mRNA stems from differential association of Argonaute with other proteins. This seems to primarily affect the relative contribution of translation inhibition vs. mRNA destabilization. In particular, the larger differences appear to occur between the germline or early embryo versus somatic tissues. In C. elegans, the prevalent form of miRISC in the germline has been shown to lack the GW182 proteins AIN-1 and AIN-2 and instead associates with P-granule constituents. The resulting recruitment of target mRNAs to P-granules inhibits protein production but does not promote mRNA decay. This has been proposed to protect maternal mRNAs whose translation products are not beneficial in the germline but are required in the early embryo for robust development. Consistent with these observations, C. elegans embryos tolerate mutations that severely impede association of Argonaute with AIN-1/2. Despite Argonautes being essential for embryonic development of C. elegans, AIN-1/2 play a secondary role at this stage. However, the interaction between Argonaute and the GW182 orthologs is necessary for post-embryonic development.

37GW182-independent function of miRISC has also been observed in other contexts. For instance, in Drosophila S2 cells, induction of mitogenic signaling via serum withdrawal results in formation of an ER-associated, GW182-independent miRISC. This complex is a potent inhibitor of translation but has no effect on mRNA deadenylation and decay. In line with this, depletion of GW182 in Drosophila S2 cells abolished miRNA-dependent deadenylation but had practically no effect on translation repression. The diversity in miRNA mediated silencing mechanisms provides organisms with enhanced capacity for gene regulation, while posing additional challenges for a complete understanding of miRNA functions in vivo.

38Animals like C. elegans have adopted variant miRNA activity in the germline, yet other animals seem to have evolved ways to dampen or abolish germline miRNA activity altogether. In Drosophila oocytes, Ago-1 is present at very low levels and only increases upon maternal to zygotic transition, coinciding with the production of a miRNA cluster involved in maternal mRNA decay. Zebrafish zygotes also have low miRNA levels, with considerable accumulation starting around the blastula stage. At that time, miRNAs are also involved in the maternal to zygotic transition. Most notably, miR-430 is expressed at the onset of zygotic genome activation and promotes maternal mRNA clearance. The mouse germline also appears to lack essential miRNA functions, as depletion of DGCR8 results in normal oocytes that give rise to healthy offspring upon fertilization with wild-type sperm. In the absence of both maternal and zygotic DGCR8, zygotes still undergo normal pre-implantation development but then arrest prior to E6.5. Clearly, miRNA-mediated regulation plays important roles in early animal development, yet the contribution and mechanisms of action in the developmental window around fertilization remain an active area of investigation.

39miRNAs provide an outstanding way to confer specificity to a variety of repressor complexes. Different effector mechanisms may operate within one organism, or even within one cell, and may be dynamically regulated under different conditions. It will be interesting to find out how different modes of regulation are used in different cellular contexts within animal development and physiology.

40In the course of animal evolution, the miRNA repertoire expanded drastically in conjunction with complexity (;;;;;; Figure 5). Often, miRNAs arose in bursts coinciding with major organismal innovations, for example the emergence of vertebrates, or cortical expansion in primates. While the animal miRNA machinery originated in unicellular holozoans, the most conserved animal miRNA, miR-100, first appeared in the last common ancestor of cnidarians and bilateria. Organisms diverging early in eukaryotic evolution tend to have few, mostly non-conserved miRNA genes, indicating a high evolutionary flux in basal clades. The availability of high-quality miRNA annotations in diverse genomes has recently upgraded our ability to place miRNAs into an evolutionary context. This opens up exciting new avenues, enabling connections between miRNA age, expression and function during development, as well as the emergence of specific features at the organismal level.

41A widespread view in the field is that miRNAs tend to be rapidly gained and lost in the course of evolution, although part of this has been recently challenged. Nevertheless, a substantial number of miRNAs have acquired important functions and remain conserved. Because miRNA evolution is intimately connected to evolution of target genes, conservation of miRNAs is observed primarily over the seed region, which determines targeting specificity. However, features beyond the seed can critically impact miRNA function, underscored by the observation that some mature miRNAs are conserved from the first to the last nucleotide across large evolutionary distances. For example, let-7 has not accumulated a single mutation between humans and worms, or mir-9a, has remained identical between Drosophila, mouse, and human.

42miRNAs are much younger than protein coding genes (on average 169 Myr vs. 1195 Myr respectively), and many of them arose more recently, after the split of diverse phylogenetic groups. For instance, an estimated 46% of human miRNAs are primate-specific and 14% are human-specific. In general, miRNA genes evolve de novo from hairpin-structures located within introns or intergenic regions, which in turn likely originate through one of three proposed models: (i) inverted gene duplication of a gene that will subsequently become target of the miRNA; (ii) transposon-insertion followed by derivatization; and (iii) spontaneous evolution out of random sequences. However, the majority of functionally important miRNAs arose from duplications of existing miRNAs.

43Diversification of the miRNA repertoire occurs both through the addition of new miRNAs and the addition or change in targets. An improved understanding of the latter will require better knowledge of what are the biologically meaningful targets of any given miRNA. Whereas for a few miRNAs we know of a number of experimentally well-defined targets, for most miRNAs we rely on computational prediction algorithms. Because such prediction tools yield numerous false positives, substantial experimental validation of targets will be necessary for a deeper understanding of how miRNA-target interactions change over time.

44Duplication followed by sequence diversification of miRNAs can lead to target diversification, changes in expression pattern, and pronounced increases in dose. In many cases, if the seed sequence is retained, miRNA gene duplication marks the birth of a (homo-seed) miRNA family. Members of a family function largely redundantly on a shared set of target mRNAs. In many cases the full extent of the function of miRNA family becomes apparent only upon removing all members. Curiously, most animal miRNAs whose loss of function causes severe defects, occur in families with sometimes extreme copy numbers. In C. elegans, two miRNA families are required for completion of embryonic development: the MIR-36 family (8 members in C. elegans, 29 members in the closely related C. briggsae) and MIR-100 family (miR-51-56 in the worm). In zebrafish, MIR-430, which plays an outstanding role during embryonic development, has evolved at least 57 family members (according to mirgenedb2.0) located within a 16 kb region on chromosome 4. Mouse embryos lacking the miR-290-295 and miR-302-367 clusters (mammalian miR-430 homologs) arrest early in embryogenesis, with defects that are only partially recapitulated if one or the other family is removed.

45Underscoring the biological significance of miRNA duplication followed by organization into families, there seems to be an expansive trend among miRNAs with important biological functions. Potential reasons include (i) increasing the dose of mature miRNA to enhance efficient target silencing, or (ii) evolutionary robustness and flexibility, e.g., mutations in one family member are not immediately detrimental, and individual copies can be further diversified in sequence or in expression pattern. Different family members share identical seed sequences, and in some cases, paralogous miRNAs are also conserved around nucleotides 13–17, which underscores the contribution of these positions to efficient targeting. However, in other cases family members differ in sequences beyond the seed, which can affect targeting properties but also biogenesis or loading efficiency as discussed above. Thus, while miRNA family members appear largely redundant, individual members can acquire specific functions.

46A recent analysis found that out of 352 human miRNAs that are conserved among vertebrates, 207 (58.8%) are duplicates and 125 (35.5%) are homo-seed family miRNAs. miRNAs in families differ from singletons in their evolutionary dynamics and functional roles, with family miRNAs tending to be: (i) older than singletons, (ii) more conserved at the sequence level than singletons, (iii) enriched for diverse expression in distinct tissues, (iv) broader in target range, and (v) implicated in more diseases. These functional correlations are still significant, albeit less pronounced, when family vs. singleton miRNAs are stratified by age, with older miRNAs tending to contribute more to disease, target more genes, and being expressed in significantly more tissues. In addition, the efficiency of target repression correlates with degree of conservation as well as evolutionary age for many miRNAs.

47The expansion of metazoan miRNAs was likely one of the factors that contributed to the evolution of complexity in present-day animals. In this context, de novo evolution but also miRNA duplication followed by sequence diversification played an important role laying the foundation for miRNA families. Among others, family membership and evolutionary age of miRNAs coincides with functional trends, offering a useful context for elucidating the contribution of miRNAs to animal development and homeostasis. Nonetheless, clade-specific singleton miRNAs also provide a source of innovation. For example, miR-791 originated in a class of nematodes called Chromadorea, and at least in C. elegans it acquired an important function in its CO2-sensing neurons. Similarly, lsy-6 originated in the last Caenorhabditis common ancestor and plays an essential role in sensory neuron diversification in C. elegans.

48Since the discovery of miRNAs, the field has made tremendous progress toward understanding the molecular mechanisms of biogenesis and action of this versatile class of repressors. The vast majority of these mechanistic studies have been performed in cell culture models, in which biochemical approaches are feasible. This has given us detailed snapshots of the possible roles of miRNAs at the molecular and cellular levels. At the organismal level however, most of our understanding comes from genetics, either from manipulations of the miRNA biogenesis machinery or individual miRNAs. While it is clear that miRNAs are necessary for the correct development and function of multiple cell types, in most cases we do not understand the functionally relevant relationships of miRNAs and their targets, the consequences on gene regulatory networks, and how the effect on specific cell types impacts the organism. Given the broad implication of miRNAs in physiology and disease, a deeper mechanistic understanding of the roles of miRNAs within complex organisms is highly desirable. We expect that new technologies that enable this depth of analysis in animals will make this possible.

49PD and LC wrote the manuscript. PD designed, drew, and painted the figures in ink and watercolor.

50The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.