Evidence that microRNAs are part of the molecular toolkit regulating adult reproductive diapause in the mosquito, Culex pipiens

MicroRNAs in the developmental toolbox - a comparative approach to understanding their role in regulating insect development

MicroRNAs are ubiquitous in the genomes of metazoans. Since their discovery during the late 20th century, our understanding of these small, noncoding RNAs has grown rapidly. However, there are still many unknowns about the functional significance of miRNAs - especially in non-model insects. Here I discuss the accumulating evidence that microRNAs are part of gene regulatory networks that determine not only the developmental outcome but also mediate transitions between stages and alternative developmental pathways. During the last 20 years, researchers have published a multitude of profiling studies that describe changes in miRNAs that may be important for development and catalog potential targets. Proof-of-principle studies document phenotypic changes that occur when candidate genes and/or miRNAs are inhibited or overexpressed. Studies that use both of these approaches, along with methods for confirming miRNA-mRNA interaction, demonstrate the necessary roles for miRNAs within gene networks. Together, all of these types of studies provide essential clues for understanding the function of miRNAs in the developmental toolbox.

Light pollution disrupts seasonal reproductive phenotypes and reduces lifespan in the West Nile vector, Culex pipiens

Females of the Northern House mosquito, Culex pipiens, are important disease vectors as they transmit pathogens including West Nile virus. These females survive the winter by entering diapause, a state of dormancy, characterized by the accumulation of lipids, cessation of blood-feeding, and reproductive arrest. Diapause is cued by photoperiod, so as days become short in late summer and early fall, female Cx. pipiens prepare to overwinter and disease transmission decreases. We previously demonstrated that Artificial light at night (ALAN) causes female Cx. pipiens to avert diapause and continue to blood-feed when reared under short-day conditions. Additionally, light pollution alters seasonal differences in mosquito activity and nutrient reserves. However, it is unclear how exposure to ALAN affects blood-feeding and fecundity in long-day reared females, as well as the survival of Cx. pipiens exposed under both short and long-day conditions. In this study, we hypothesized that females exposed to ALAN in long-day conditions would have a lower proclivity to blood-feed, reduced fecundity, and reduced survival. Results from our lab-based experiments demonstrate that females exposed to ALAN in long-day conditions were less likely to blood-feed but were more fecund than long-day reared females that were not exposed to ALAN, and that ALAN exposure did not affect lifespan of long-day reared females. Additionally, we hypothesized ALAN exposure under short-day conditions would reduce survival, and our data supports this hypothesis. Overall, our results demonstrate that ALAN is an important urban stressor that has the potential to affect reproduction and lifespan in mosquitoes, and therefore has the potential to create evolutionary tradeoffs.

Differentially expressed microRNAs in brains of adult females may regulate the maternal block of diapause in Sarcophaga bullata

The maternal regulation of diapause is one type of phenotypic plasticity where the experience of the mother leads to changes in the phenotype of her offspring that impact how well-suited they will be to their future environment. Sarcophaga bullata females with a diapause history produce offspring that cannot enter diapause even if they are reared in a diapause inducing environment. Accumulating evidence suggests that microRNAs regulate diapause and, possibly, maternal regulation of diapause. We found significant differences in the abundances of several microRNAs (miR-125-5p, miR-124-3p, miR-31-5p, and miR-277-3p) in brains dissected from adult female S. bullata that had experienced diapause compared to females with no diapause history. We also found moderate differences in the mRNA expression of the circadian-clock related genes, clock, clockwork orange, and period. MiR-124-3p and miR-31-5p are part of a gene network that includes these circadian clock-related genes. Taken together our results suggest the maternal block of diapause in S. bullata is regulated, at least in part, by a network that includes microRNAs and the circadian clock.

A glimpse into the world of microRNAs and their putative roles in hard ticks

Ticks are important blood feeding ectoparasites that transmit pathogens to wildlife, domestic animals, and humans. Hard ticks can feed for several days to weeks, nevertheless they often go undetected. This phenomenon can be explained by a tick's ability to release analgesics, immunosuppressives, anticoagulants, and vasodilators within their saliva. Several studies have identified extracellular vesicles (EVs) as carriers of some of these effector molecules. Further, EVs, and their contents, enhance pathogen transmission, modulate immune responses, and delay wound healing. EVs are double lipid-membrane vesicles that transport intracellular cargo, including microRNAs (miRNAs) to recipient cells. miRNAs are involved in regulating gene expression post-transcriptionally. Interestingly, tick-derived miRNAs have been shown to enhance pathogen transmission and affect vital biological processes such as oviposition, blood digestion, and molting. miRNAs have been found within tick salivary EVs. This review focuses on current knowledge of miRNA loading into EVs and homologies reported in ticks. We also describe findings in tick miRNA profiles, including miRNAs packed within tick salivary EVs. Although no functional studies have been done to investigate the role of EV-derived miRNAs in tick feeding, we discuss the functional characterization of miRNAs in tick biology and pathogen transmission. Lastly, we propose the possible uses of tick miRNAs to develop management tools for tick control and to prevent pathogen transmission. The identification and functional characterization of conserved and tick-specific salivary miRNAs targeting important molecular and immunological pathways within the host could lead to the discovery of new therapeutics for the treatment of tick-borne and non-tick-borne human diseases.

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

Dormancy is a key feature of stem cell function in adult tissues as well as in embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state remains unclear. Here we show that microRNA activity, which is otherwise dispensable for preimplantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in the loss of pluripotent cells. Through the integration of high-sensitivity small RNA expression profiling of individual embryos and protein expression of miRNA targets with public data of protein-protein interactions, we constructed the miRNA-mediated regulatory network of mouse early embryos specific to diapause. We find that individual miRNAs contribute to the combinatorial regulation by the network, and the perturbation of the network compromises embryo survival in diapause. We further identified the nutrient-sensitive transcription factor TFE3 as an upstream regulator of diapause-specific miRNAs, linking cytoplasmic MTOR activity to nuclear miRNA biogenesis. Our results place miRNAs as a critical regulatory layer for the molecular rewiring of early embryos to establish dormancy.

A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi

Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics. Here we aim to advance our understanding of diapause by investigating microRNA (miRNA) expression in diapausing and direct developing pupae of the butterfly Pieris napi. We identified coordinated patterns of miRNA expression throughout diapause in both head and abdomen tissues of pupae, and via miRNA target identification, found several expression patterns to be enriched for relevant diapause-related physiological processes. We also identified two candidate miRNAs, miR-14-5p and miR-2a-3p, that are likely involved in diapause progression through their activity in the ecdysone pathway, a critical regulator of diapause termination. miR-14-5p targets phantom, a gene in the ecdysone synthesis pathway, and is upregulated early in diapause. miR-2a-3p has been found to be expressed in response to ecdysone, and is upregulated during diapause termination. Together, the expression patterns of these two miRNAs match our current understanding of the timing of hormonal regulation of diapause in P. napi and provide interesting candidates to further explore the mechanistic role of microRNAs in diapause regulation.

An RNAi screen for conserved kinases that enhance microRNA activity after dauer in Caenorhabditis elegans

Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes posttranscriptionally through the activity of the microRNA-induced silencing complex. Argonaute is the core microRNA-induced silencing complex protein that binds to both the microRNA and to other microRNA-induced silencing complex proteins. The 2 major microRNA Argonautes in the Caenorhabditis elegans soma are ALG-1 and ALG-2, which function partially redundantly. Loss of alg-1 [alg-1(0)] causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent if alg-1(0) animals undergo a diapause stage called dauer. Levels of the relevant microRNAs are not higher during or after dauer, suggesting that activity of the microRNA-induced silencing complex may be enhanced in this context. To identify genes that are required for alg-1(0) mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating microRNA-induced silencing complex activity. We found RNAi knockdown of 4 kinase-encoding genes, air-2, bub-1, chk-1, and nekl-3, caused vulval defects and reiterative phenotypes in alg-1(0) mutants after dauer, and that these defects were more penetrant in an alg-1(0) background than in wild type. Our results implicate these kinases as potential regulators of microRNA-induced silencing complex activity during postdauer development in C. elegans.

Role of miR-276-3p in the cyantraniliprole resistance mechanism of Bemisia tabaci via CYP6CX3 targeting

The sweet potato whitefly, Bemisia tabaci, is an important insect pest that transmits over 200 different plant viruses and causes serious damage to the production of cotton and Solanaceae vegetables. Cyantraniliprole is the first diamide insecticide, showing toxicity against B. tabaci. However, B. tabaci has developed resistance to this insecticide by upregulating the expressions of cytochrome P450 genes such as CYP6CX3, while there is limited information on the regulatory mechanism mediated by miRNA. In the present study, ten miRNAs were predicted to target CYP6CX3, in which miR-276-3p showed an inverse expression pattern with CYP6CX3 in two cyantraniliprole resistant strains and under cyantraniliprole exposure. A luciferase assay demonstrated that miR-276-3p suppressed CYP6CX3 expression by pairing with residues 1445-1453. Overexpression or knockdown of miR-276-3p directly impacted B. tabaci resistance to cyantraniliprole. In addition, exposure to cyantraniliprole led to a significant reduction in the expressions of five genes (drosha, dicer1, dicer2, Ago1, and Ago2A) associated with miRNA biogenesis. Suppressing genes such as drosha, dicer1, and Ago2A reduced the expression of miR-276-3p, increased CYP6CX3 expression, and decreased B. tabaci resistance to cyantraniliprole. These results improve our understanding of the role of miRNAs in P450 regulation and cyantraniliprole resistance in B. tabaci.

The importance of fat accumulation and reserves for insect overwintering

Winter is a challenging season for ectothermic species such as insects. In addition to thermal stress imposed by cold temperatures, food scarcity during winter can lead to starvation and energy drain. In preparation for winter, most insects accumulate lipid (fat) reserves, which are the principal source of energetic fuel during overwintering. In this review, we highlight the most recent literature on lipid metabolism in response to cold. We first discuss how lipid metabolism is affected by biotic and abiotic environmental changes in preparation for winter. We then highlight how lipid dynamics are affected during winter, including physiological and (epi)genetic mechanisms. We end our review emphasizing the importance of remaining fat reserves in spring and how climate change can negatively impact lipid metabolism and fitness.

RNA N6-methyladenosine of DHAPAT and PAP involves in regulation of diapause of Bombyx mori via the lipid metabolism pathway

Environment-induced epigenetics are involved in diapause regulation, but the molecular mechanism that epigenetically couples nutrient metabolism to diapause regulation remains unclear. In this study, we paid special attention to the significant differences in the level of N6-adenosine methylation (m6A) of dihydroxyacetone phosphate acyltransferase (DHAPAT) and phosphatidate phosphatase (PAP) genes in the lipid metabolism pathway of the bivoltine silkworm (Bombyx mori) strain Qiufeng developed from eggs incubated at a normal temperature (QFHT, diapause egg producer) compared to those from eggs incubated at a low temperature (QFLT, non-diapause egg producer). We knocked down DHAPAT in the pupal stage of the QFLT group, resulting in the non-diapause destined eggs becoming diapausing eggs. In the PAP knockdown group, the colour of the non-diapause destined eggs changed from light yellow to pink 3 days after oviposition, but they hatched as normal. Moreover, we validated that YTHDF3 binds to m6A-modified DHAPAT and PAP mRNAs to promote their stability and translation. These results suggest that RNA m6A methylation participates in the diapause regulation of silkworm by changing the expression levels of DHAPAT and PAP and reveal that m6A epigenetic modification can be combined with a lipid metabolism signal pathway to participate in the regulation of insect diapause traits, which provides a clearer image for exploring the physiological basis of insect diapause.

Epigenetic effects of climate change on insects

Climate change has been causing severe modifications to the environment that are predicted to aggravate in the future, which create critical challenges for insects to cope. Populations can respond to the changes depending on the standing genetic variation. Additionally, they could potentially rely on epigenetic mechanisms as a source of phenotypic variation. These mechanisms can influence gene regulation and can respond to the external environment, being implicated in phenotypic plasticity. Thus, epigenetic variation could be advantageous in changing, unpredictable environments. However, little is known about causal relationships between epigenetic marks and insects' phenotypes, and whether the effects are truly beneficial to the fitness. Empirical studies are now urgent to better understand whether epigenetic variation can help or hinder insect populations facing climate change.

Integrated miRNA and transcriptome profiling to explore the molecular mechanism of Spodoptera frugiperda larval midgut in response to azadirachtin exposure

As a destructive agricultural pest, Spodoptera frugiperda has spread worldwide in the past few years. Azadirachtin, an environmentally friendly and most promising compound, showed adverse effects, including mortality and growth inhibition, against S. frugiperda. While the effects of azadirachtin on the midgut of this pest remain to be determined. In this study, structural damage was observed in the larval midguts of S. frugiperda with azadirachtin exposure. RNA-seq on the larval midguts with different azadirachtin treatments was performed. Compared to the control group, a total of 3344 and 4759 differentially expressed genes (DEGs) were identified in the midguts with 0.1 and 0.5 μg/g azadirachtin exposure, respectively. Among them, the DEGs encoding detoxification enzymes/proteins, immune-related proteins, digestion and absorption-related proteins, and transcript factors were further analyzed. High-throughput sequencing was also used for the identification of differentially expressed microRNAs in different treatments. A total of 153 conserved miRNAs and 147 novel miRNAs were identified, of which 11 and 29 miRNAs were affected by 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The integrated analysis found that 13 and 178 miRNA versus mRNA pairs were acquired in the samples with 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The results of high-throughput sequencing were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). These results provide useful information for revealing the molecular mechanism of S. frugiperda larval midgut in response to azadirachtin.

MicroRNA let-7-5p targets the juvenile hormone primary response gene Krüppel homolog 1 and regulates reproductive diapause in Galeruca daurica

MicroRNAs (miRNAs) regulate various biological processes in insects. However, their roles in the regulation of insect diapause remain unknown. In this study, we address the biological function of a conserved miRNA, let-7-5p in the regulation of a juvenile hormone primary response gene, Krüppel homolog 1 (Kr-h1), which modulates reproductive diapause in Galeruca daurica. The dual luciferase reporter assay showed that let-7-5p depressed the expression of Kr-h1. The expression profiles of let-7-5p and Kr-h1 displayed opposite patterns in the adult developmental stage. Injection of let-7-5p agomir in pre-diapause adult females inhibited the expression of Kr-h1, which consequently led to delay ovarian development, increase lipid accumulation, expand fat body, and induce reproductive diapause just as depleting Kr-h1 did. Conversely, injection of let-7-5p antagomir resulted in opposite effects by reducing fat storage and stimulating reproduction. Moreover, JH receptor agonist methoprene reduced the expression of let-7-5p, and rescued the ovarian development defects associated with let-7-5p overexpression. These results indicate that let-7-5p plays an important role in the regulation of reproductive diapause and development of G. daurica adults through its target gene Kr-h1.

Temporal analysis of microRNAs associated with wing development in the English grain aphid, Sitobion avenae (F.) (Homoptera: Aphidiae)

Molecular mechanisms underlying wing evolution and development have been a point of scientific inquiry for decades. Phloem-feeding aphids are one of the most devastating global insect pests, where dispersal of winged morphs lead to annual movements, migrations, and range expansions. Aphids show a polyphenic wing dimorphism trait, and offer a model to study the role of environment in determining morphological plasticity of a single genotype. Despite recent progresses in the genetic understanding of wing polyphenism, the influence of environmental cues remains unclear. To investigate the involvement of miRNAs in wing development, we sequenced small RNA libraries of the English grain aphid, Sitobion avenae (F.) across six different developmental stages. As a result, we identified 113 conserved and 193 S. avenae-specific miRNAs. Gene Ontology and KEGG pathway analyses of putative target mRNAs for the six differentially expressed miRNAs are enriched for wing development processes. Dietary uptake of miR-263a, miR-316, and miR-184a agomirs and antagomirs led to significantly higher mortality (>70%) and a lower proportion of winged morphs (<5%). On the other hand, wing malformation was observed in miR-2 and miR-306 agomirs and miR-2 and miR-14 antagomirs, respectively, suggesting their involvement in S. avenae wing morphogenesis. These combined results not only shed light on the regulatory role of miRNAs in wing dimorphism, but also provide potential novel targets for the long-term sustainable management of S. avenae, a devastating global grain pest.

Hormonal Regulation of Diapause and Development in Nematodes, Insects, and Fishes

Diapause is a state of developmental arrest adopted in response to or in anticipation of environmental conditions that are unfavorable for growth. In many cases, diapause is facultative, such that animals may undergo either a diapause or a non-diapause developmental trajectory, depending on environmental cues. Diapause is characterized by enhanced stress resistance, reduced metabolism, and increased longevity. The ability to postpone reproduction until suitable conditions are found is important to the survival of many animals, and both vertebrate and invertebrate species can undergo diapause. The decision to enter diapause occurs at the level of the whole animal, and thus hormonal signaling pathways are common regulators of the diapause decision. Unlike other types of developmental arrest, diapause is programmed, such that the diapause developmental trajectory includes a pre-diapause preparatory phase, diapause itself, recovery from diapause, and post-diapause development. Therefore, developmental pathways are profoundly affected by diapause. Here, I review two conserved hormonal pathways, insulin/IGF signaling (IIS) and nuclear hormone receptor signaling (NHR), and their role in regulating diapause across three animal phyla. Specifically, the species reviewed are Austrofundulus limnaeus and Nothobranchius furzeri annual killifishes, Caenorhabditis elegans nematodes, and insect species including Drosophila melanogaster, Culex pipiens, and Bombyx mori. In addition, the developmental changes that occur as a result of diapause are discussed, with a focus on how IIS and NHR pathways interact with core developmental pathways in C. elegans larvae that undergo diapause.

Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance

The diamondback moth (DBM), Plutella xylostella, one of the most destructive lepidopteran pests worldwide, has developed field resistance to Bacillus thuringiensis (Bt) Cry toxins. Although miRNAs have been reported to be involved in insect resistance to multiple insecticides, our understanding of their roles in mediating Bt resistance is limited. In this study, we constructed small RNA libraries from midguts of the Cry1Ac-resistant (Cry1S1000) strain and the Cry1Ac-susceptible strain (G88) using a high-throughput sequencing analysis. A total of 437 (76 known and 361 novel miRNAs) were identified, among which 178 miRNAs were classified into 91 miRNA families. Transcripts per million analysis revealed 12 differentially expressed miRNAs between the Cry1S1000 and G88 strains. Specifically, nine miRNAs were down-regulated and three up-regulated in the Cry1S1000 strain compared to the G88 strain. Next, we predicted the potential target genes of these differentially expressed miRNAs and carried out GO and KEGG pathway analyses. We found that the cellular process, metabolism process, membrane and the catalytic activity were the most enriched GO terms and the Hippo, MAPK signaling pathway might be involved in Bt resistance of DBM. In addition, the expression patterns of these miRNAs and their target genes were determined by RT-qPCR, showing that partial miRNAs negatively while others positively correlate with their corresponding target genes. Subsequently, novel-miR-240, one of the differentially expressed miRNAs with inverse correlation with its target genes, was confirmed to interact with Px017590 and Px007885 using dual luciferase reporter assays. Our study highlights the characteristics of differentially expressed miRNAs in midguts of the Cry1S1000 and G88 strains, paving the way for further investigation of miRNA roles in mediating Bt resistance.

Comparative Transcriptome Analysis Reveals bmo-miR-6497-3p Regulate Circadian Clock Genes during the Embryonic Diapause Induction Process in Bivoltine Silkworm

Diapause is one of the survival strategies of insects for confronting adverse environmental conditions. Bombyx mori displays typical embryonic diapause, and offspring diapause depends on the incubation environment of the maternal embryo in the bivoltine strains of the silkworm. However, the molecular mechanisms of the diapause induction process are still poorly understood. In this study, we compared the differentially expressed miRNAs (DEmiRs) in bivoltine silkworm embryos incubated at diapause- (25 °C) and non-diapause (15 °C)-inducing temperatures during the blastokinesis (BK) and head pigmentation (HP) phases using transcriptome sequencing. There were 411 known miRNAs and 71 novel miRNAs identified during the two phases. Among those miRNAs, there were 108 and 74 DEmiRs in the BK and HP groups, respectively. By the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the predicted target genes of the DEmiRs, we found that aside from metabolism, the targets were also enriched in phototransduction-fly and insect hormone biosynthesis in the BK group and the HP group, respectively. Dual luciferase reporter assay illustrated that bmo-miR-6497-3p directly regulated Bmcycle and subsequently regulated the expression of circadian genes. These results imply that microRNAs, as vitally important regulators, respond to different temperatures and participate in the diapause induction process across species.

Molecular Regulation of Paused Pluripotency in Early Mammalian Embryos and Stem Cells

The energetically costly mammalian investment in gestation and lactation requires plentiful nutritional sources and thus links the environmental conditions to reproductive success. Flexibility in adjusting developmental timing enhances chances of survival in adverse conditions. Over 130 mammalian species can reversibly pause early embryonic development by switching to a near dormant state that can be sustained for months, a phenomenon called embryonic diapause. Lineage-specific cells are retained during diapause, and they proliferate and differentiate upon activation. Studying diapause thus reveals principles of pluripotency and dormancy and is not only relevant for development, but also for regeneration and cancer. In this review, we focus on the molecular regulation of diapause in early mammalian embryos and relate it to maintenance of potency in stem cells in vitro. Diapause is established and maintained by active rewiring of the embryonic metabolome, epigenome, and gene expression in communication with maternal tissues. Herein, we particularly discuss factors required at distinct stages of diapause to induce, maintain, and terminate dormancy.

Development of miRNA-Based Approaches to Explore the Interruption of Mosquito-Borne Disease Transmission

MicroRNA (miRNA or miR)-based approaches to interrupt the transmission of mosquito-borne diseases have been explored since 2005. A review of these studies and areas in which to proceed is needed. In this review, significant progress is reviewed at the level of individual miRNAs, and miRNA diversification and relevant confounders are described in detail. Current miRNA studies in mosquitoes include four steps, namely, identifying miRNAs, validating miRNA-pathogen interactions, exploring action mechanisms, and performing preapplication investigations. Notably, regarding the Plasmodium parasite, mosquito miRNAs generally bind to mosquito immunity- or development-related mRNAs, indirectly regulating Plasmodium infection; However, regarding arboviruses, mosquito miRNAs can bind to the viral genome, directly modifying viral replication. Thus, during explorations of miRNA-based approaches, researchers need select an ideal miRNA for investigation based on the mosquito species, tissue, and mosquito-borne pathogen of interest. Additionally, strategies for miRNA-based approaches differ for arboviruses and protozoan parasites.

Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites. Filtering the non-coding genome to uncover these functional elements is an expanding area of research, though identification of non-coding regulatory elements is challenging due to the lack of an amino acid-like code for the non-coding genome and a lack of sequence conservation across species. This review focuses on three types of non-coding regulatory elements: (1) microRNAs (miRNAs), (2) long non-coding RNAs (lncRNAs), and (3) enhancers, and summarizes current advances in technical and analytical approaches for measurement of each of these elements on a genome-wide scale. The review also summarizes and highlights novel findings following application of these techniques in mosquito-borne disease research. Looking beyond the protein-coding genome is essential for understanding the complexities that underlie differential gene expression in response to arboviral or parasite infection in mosquito disease vectors. A comprehensive understanding of the regulation of gene and protein expression will inform transgenic and other vector control methods rooted in naturally segregating genetic variation.

Epigenetic Molecular Mechanisms in Insects

Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.

MicroRNA-277 regulates dopa decarboxylase to control larval-pupal and pupal-adult metamorphosis of Helicoverpa armigera

Insect metamorphosis is a complex process involving many metabolic pathways, such as juvenile hormones and molting hormones, bioamines, microRNAs (miRNAs), etc. However, relatively little is known about the biogenic amines and their miRNAs to regulate cotton bollworm metamorphosis. Here we show that one miRNA, miR-277 regulates larval-pupal and pupal-adult metamorphosis of cotton bollworm by targeting the 3'UTR of Dopa decarboxylase (DDC), a synthetic catalytic enzyme of dopamine. Injection of miR-277 agomir inhibited the expression of DDC at the mRNA and protein levels, leading to defects in the pupation and emergence of H. armigera that was consistent with the phenotype obtained by injection of DDC double-stranded RNA (dsRNA). Injection of miR-277 antagomir induced the mRNA and protein expression of DDC and rescued the phenotype of pupation failure caused by DDC gene silencing. Unexpectedly, miR-277 antagomir can also cause failure of emergence of H. armigera and both agomir and antagomir of miR-277 injection could cause abnormal phenotypes in wing veins. This study reveals that elaborate regulation of miRNA and its target gene expression is prerequisite for insect development, which provides a new insight to study the developmental mechanisms of insect wing veins.

Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks

Insect population dynamics are closely related to 'human' ecological and economic environments, and a central focus of research is outbreaks. However, the lack of molecular-based investigations restricts our understanding of the intrinsic mechanisms responsible for insect outbreaks. In this context, the moth Dendrolimus punctatus Walker can serve as an ideal model species for insect population dynamics research because it undergoes periodic outbreaks. Here, high-throughput whole-transcriptome sequencing was performed using D. punctatus, sampled during latent and outbreak periods, to systemically explore the molecular basis of insect outbreaks and to identify the involved non-coding RNA (ncRNA) regulators, namely microRNAs, long non-coding RNAs, and circular RNAs. Differentially expressed mRNAs of D. punctatus from different outbreak periods were involved in developmental, reproductive, immune, and chemosensory processes; results that were consistent with the physiological differences in D. punctatus during differing outbreak periods. Targets analysis of the non-coding RNAs indicated that long non-coding RNAs could be the primary ncRNA regulators of D. punctatus outbreaks, while circular RNAs mainly regulated synapses and cell junctions. The target genes of differentially expressed microRNAs mainly regulated the metabolic and reproductive pathways during the D. punctatus outbreaks. Developmental, multi-organismal, and reproductive processes, as well as biological adhesion, characterized the competing endogenous RNA network. Chemosensory and immune genes closely related to the outbreak of D. punctatus were further analyzed in detail: from their ncRNA regulators' analysis, we deduce that both lncRNA and miRNA may play significant roles. This is the first report to examine the molecular basis of coding and non-coding RNAs' roles in insect outbreaks. The results provide potential biomarkers for control targets in forest insect management, as well as fresh insights into underlying outbreak-related mechanisms, which could be used for improving insect control strategies in the future.

Circadian transcription factors differentially regulate features of the adult overwintering diapause in the Northern house mosquito, Culex pipiens

The short days of late summer and early fall are the environmental cues that most temperate insects and other animals use to predict winter's arrival. Although it is still unclear precisely how insects measure daylength, there is mounting evidence that the circadian clock regulates seasonal responses including photoperiodic diapause. Females of the Northern house mosquito, Culex pipiens, enter an adult reproductive diapause in response to short daylengths. While in this state, females divert their resources from reproduction to survival, arresting egg follicle development and increasing fat content. Here, we characterized the expression profile of two circadian transcription factors, vrille (vri) and Par domain protein 1 (Pdp1), as well as genes downstream of the clock, takeout (to) and Nocturnin (Noc) and under different seasonal conditions. We saw that while vri mRNA oscillated under both long day and short day conditions, Pdp1 expression oscillated only under long day conditions and was constitutively upregulated in diapausing females. We saw similar expression profiles for to and Noc, suggesting that PDP1 might regulate their expression or that Pdp1, to and Noc might be regulated by the same transcription factor. We suppressed vri and Pdp1 using RNA interference. dsRNA against vri provided inconsistent results, sometimes stimulating autogenous egg follicle development in both long and short day-reared females, and other times had no effect. In contrast, knocking down Pdp1 prevented short day-reared females from accumulating fat reserves, but increased expression of to and Noc. Taken together, these data suggest that the circadian transcription factors Vri and Pdp1 may independently regulate signaling pathways underlying arrested egg follicle development and fat accumulation in diapausing females of Cx. pipiens.

Seasonal phenotype-specific expression of microRNAs during metamorphosis in the European map butterfly Araschnia levana

The European map butterfly (Araschnia levana) is a well-known example of seasonal polyphenism because the spring and summer imagoes exhibit distinct morphological phenotypes. The day length and temperature during larval and prepupal development determine whether spring or summer imagoes emerge after metamorphosis. Inspired by the fundamentally different transcriptomic profiles in prepupae developing from larvae exposed to long days or short days, we postulate that posttranscriptional epigenetic regulators such as microRNAs (miRNAs) may contribute to the epigenetic control of seasonal polyphenism in A. levana. To test this hypothesis, we used microarrays containing over 2,000 insect miRNAs to identify candidate regulators that are differentially expressed in last-instar larvae or pupae developing under long-day or short-day conditions. We used our transcriptomic database to identify potential 3'-untranslated regions of messenger RNAs to predict miRNA targets by considering both base pair complementarity and minimum free energy hybridization. This approach resulted in the identification of multiple targets of miRNAs that were differentially regulated in polyphenic morphs of A. levana including a candidate (miR-2856-3p) regulating the previously identified diapause bioclock protein gene. In conclusion, the expression profiling of miRNAs provided insights into their possible involvement in seasonal polyphenism of A. levana and offer an important resource for further studies.

Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals

Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.