miR-210 controls the evening phase of circadian locomotor rhythms through repression of Fasciclin 2

NF-κB factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210

MicroRNAs (miRNAs) play crucial regulatory roles in controlling immune responses, but their dynamic expression mechanisms are poorly understood. Here, we firstly confirm that the conserved miRNA miR-210 negatively regulates innate immune responses of Drosophila and human via targeting Toll and TLR6, respectively. Secondly, our findings demonstrate that the expression of miR-210 is dynamically regulated by NF-κB factor Dorsal in immune response of Drosophila Toll pathway. Thirdly, we find that Dorsal-mediated transcriptional inhibition of miR-210 is dependent on the transcriptional repressor Su(Hw). Mechanistically, Dorsal interacts with Su(Hw) to modulate cooperatively the dynamic expression of miR-210 in a time- and dose-dependent manner, thereby controlling the strength of Drosophila Toll immune response and maintaining immune homeostasis. Fourthly, we reveal a similar mechanism in human cells, where NF-κB/RelA cooperates with E4F1 to regulate the dynamic expression of hsa-miR-210 in the TLR immune response. Overall, our study reveals a conservative regulatory mechanism that maintains animal innate immune homeostasis and provides new insights into the dynamic regulation of miRNA expression in immune response.

miR-2940-1 is involved in the circadian regulation of oviposition in Aedes albopictus

The vast majority of all global species have circadian rhythm cycles that allow them to adapt to natural environments. These regular rhythms are regulated by core clock genes and recent studies have also implicated roles for microRNAs in this regulation. Oviposition is an important circadian behavior in the reproductive cycle of insect vectors of diseases, and little is known about the rhythm or its regulation in mosquitoes. Aedes albopictus is a diurnal mosquito that transmits arboviruses and is the major cause of outbreaks of dengue fever in China. We analyzed the oviposition rhythm patterns of A. albopictus under different light/dark conditions and show that the mosquitoes have an oviposition peak between zeitgeber time 9 (ZT 9) and ZT 12. Furthermore, the antagomir-mediated knockdown of expression of the microRNA miR-2940-1 affected the oviposition rhythm of A. albopictus. These data support the conclusion that miR-2940-1 is involved in the regulation of oviposition rhythm in A. albopictus and provide a foundation for using oviposition rhythms as a new target for vector mosquito control.

miR-277 regulates the phase of circadian activity-rest rhythm in Drosophila melanogaster

Circadian clocks temporally organize behaviour and physiology of organisms with a rhythmicity of about 24 h. In Drosophila, the circadian clock is composed of mainly four clock genes: period (per), timeless (tim), Clock (Clk) and cycle (cyc) which constitutes the transcription-translation feedback loop. The circadian clock is further regulated via post-transcriptional and post-translational mechanisms among which microRNAs (miRNAs) are well known post-transcriptional regulatory molecules. Here, we identified and characterized the role of miRNA-277 (miR-277) expressed in the clock neurons in regulating the circadian rhythm. Downregulation of miR-277 in the pacemaker neurons expressing circadian neuropeptide, pigment dispersing factor (PDF) advanced the phase of the morning activity peak under 12 h light: 12 h dark cycles (LD) at lower light intensities and these flies exhibited less robust rhythms compared to the controls under constant darkness. In addition, downregulation of miR-277 in the PDF expressing neurons abolished the Clk gene transcript oscillation under LD. Our study points to the potential role of miR-277 in fine tuning the Clk expression and in maintaining the phase of the circadian rhythm in Drosophila.

Novel miR-108 and miR-234 target juvenile hormone esterase to regulate the response of Plutella xylostella to Cry1Ac protoxin

Insect hormones, such as juvenile hormone (JH), precisely regulate insect life-history traits. The regulation of JH is tightly associated with the tolerance or resistance to Bacillus thuringiensis (Bt). JH esterase (JHE) is a primary JH-specific metabolic enzyme which plays a key role in regulating JH titer. Here, we characterized a JHE gene from Plutella xylostella (PxJHE), and found it was differentially expressed in the Bt Cry1Ac resistant and susceptible strains. Suppression of PxJHE expression with RNAi increased the tolerance of P. xylostella to Cry1Ac protoxin. To investigate the regulatory mechanism of PxJHE, two target site prediction algorithms were applied to predict the putative miRNAs targeting PxJHE, and the resulting putative miRNAs were subsequently verified for their function targeting PxJHE using luciferase reporter assay and RNA immunoprecipitation. MiR-108 or miR-234 agomir delivery dramatically reduced PxJHE expression in vivo, whilst only miR-108 overexpression consequently increased the tolerance of P. xylostella larvae to Cry1Ac protoxin. By contrast, reduction of miR-108 or miR-234 dramatically increased PxJHE expression, accompanied by the decreased tolerance to Cry1Ac protoxin. Furthermore, injection of miR-108 or miR-234 led to developmental defects in P. xylostella, whilst injection of antagomir did not cause any obvious abnormal phenotypes. Our results indicated that miR-108 or miR-234 can be applied as potential molecular targets to combat P. xylostella and perhaps other lepidopteran pests, providing novel insights into miRNA-based integrated pest management.

Noncoding RNA Regulation of Hormonal and Metabolic Systems in the Fruit Fly Drosophila

The importance of RNAs is commonly recognised thanks to protein-coding RNAs, whereas non-coding RNAs (ncRNAs) were conventionally regarded as 'junk'. In the last decade, ncRNAs' significance and roles are becoming noticeable in various biological activities, including those in hormonal and metabolic regulation. Among the ncRNAs: microRNA (miRNA) is a small RNA transcript with ~20 nucleotides in length; long non-coding RNA (lncRNA) is an RNA transcript with >200 nucleotides; and circular RNA (circRNA) is derived from back-splicing of pre-mRNA. These ncRNAs can regulate gene expression levels at epigenetic, transcriptional, and post-transcriptional levels through various mechanisms in insects. A better understanding of these crucial regulators is essential to both basic and applied entomology. In this review, we intend to summarise and discuss the current understanding and knowledge of miRNA, lncRNA, and circRNA in the best-studied insect model, the fruit fly Drosophila.

Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

Background

ATM (ataxia-telangiectasia mutated) protein kinase is highly conserved in metazoan, and plays a critical role at DNA damage response, oxidative stress, metabolic stress, immunity, RNA biogenesis etc. Systemic profiling of ATM regulated genes, including protein-coding genes, miRNAs, and long non-coding RNAs, will greatly improve our understanding of ATM functions and its regulation. 

Results

1) differentially expressed protein-coding genes, miRNAs, and long non-coding RNAs in atm mutated flies were identified at physiological condition and after X-ray irradiation. 2) functions of differentially expressed genes in atm mutated flies, regardless of protein-coding genes or non-coding RNAs, are closely related with metabolic process, immune response, DNA damage response or oxidative stress. 3) these phenomena are persistent after irradiation. 4) there is a cross-talk regulation towards miRNAs by ATM, E2f1, and p53 during development and after irradiation. 5) knock-out flies or knock-down flies of most irradiation-induced miRNAs were sensitive to ionizing radiation.

Conclusions

We provide a valuable resource of protein-coding genes, miRNAs, and long non-coding RNAs, for understanding ATM functions and regulations. Our work provides the new evidence of inter-dependence among ATM-E2F1-p53 for the regulation of miRNAs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-022-00254-9.

The Role of microRNAs in the Drosophila Melanogaster Visual System

MicroRNAs (miRNAs) are a class of small non-coding RNAs (∼22 nucleotides in length) that negatively regulate protein-coding gene expression post-transcriptionally by targeting mRNAs and triggering either translational repression or RNA degradation. MiRNA genes represent approximately 1% of the genome of different species and it has been estimated that every miRNA can interact with an average of 200 mRNA transcripts, with peaks of 1,500 mRNA targets per miRNA molecule. As a result, miRNAs potentially play a fundamental role in several biological processes including development, metabolism, proliferation, and apoptotic cell death, both in physiological and pathological conditions. Since miRNAs were discovered, Drosophila melanogaster has been used as a model organism to shed light on their functions and their molecular mechanisms in the regulation of many biological and behavioral processes. In this review we focus on the roles of miRNAs in the fruit fly brain, at the level of the visual system that is composed by the compound eyes, each containing ∼800 independent unit eyes called ommatidia, and each ommatidium is composed of eight photoreceptor neurons that project into the optic lobes. We describe the roles of a set of miRNAs in the development and in the proper function of the optic lobes (bantam, miR-7, miR-8, miR-210) and of the compound eyes (bantam, miR-7, miR-9a, miR-210, miR-263a/b, miR-279/996), summarizing also the pleiotropic effects that some miRNAs exert on circadian behavior.

Neurofibromin 1 in mushroom body neurons mediates circadian wake drive through activating cAMP-PKA signaling

Various behavioral and cognitive states exhibit circadian variations in animals across phyla including Drosophila melanogaster, in which only ~0.1% of the brain's neurons contain circadian clocks. Clock neurons transmit the timing information to a plethora of non-clock neurons via poorly understood mechanisms. Here, we address the molecular underpinning of this phenomenon by profiling circadian gene expression in non-clock neurons that constitute the mushroom body, the center of associative learning and sleep regulation. We show that circadian clocks drive rhythmic expression of hundreds of genes in mushroom body neurons, including the Neurofibromin 1 (Nf1) tumor suppressor gene and Pka-C1. Circadian clocks also drive calcium rhythms in mushroom body neurons via NF1-cAMP/PKA-C1 signaling, eliciting higher mushroom body activity during the day than at night, thereby promoting daytime wakefulness. These findings reveal the pervasive, non-cell-autonomous circadian regulation of gene expression in the brain and its role in sleep.

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.

Post-transcriptional modulators and mediators of the circadian clock

The endogenous circadian timekeeping system drives ~24-h rhythms in gene expression and rhythmically coordinates the physiology, metabolism and behavior in a wide range of organisms. Regulation at various levels is important for the accurate functioning of this circadian timing system. The core circadian oscillator consists of an interlocked transcriptional-translational negative feedback loop (TTFL) that imposes a substantial delay between the accumulation of clock gene mRNA and its protein to generate 24-h oscillations. This TTFL mediated daily oscillation of clock proteins is further fine-tuned by post-translational modifications that regulate the clock protein stability, interaction with other proteins and subcellular localization. Emerging evidence from various studies indicates that besides TTFL and post-translational modifications, post-transcriptional regulation plays a key role in shaping the rhythmicity of mRNAs and to delay the accumulation of clock proteins in relation to their mRNAs. In this review, we summarize the current knowledge on the importance of post-transcriptional regulatory mechanisms such as splicing, polyadenylation, the role of RNA-binding proteins, RNA methylation and microRNAs in the context of shaping the circadian rhythmicity in Drosophila and mammals. In particular, we discuss microRNAs, an important player in post-transcriptional regulation of core-clock machinery, circadian neural circuit, clock input, and output pathways. Furthermore, we provide an overview of the microRNAs that exhibit diurnal rhythm in expression and their role in mediating rhythmic physiological processes.

Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock

The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.

The conserved microRNA miR-210 regulates lipid metabolism and photoreceptor maintenance in the Drosophila retina

Increasing evidence suggests that miRNAs play important regulatory roles in the nervous system. However, the molecular mechanisms of how specific miRNAs affect neuronal development and functions remain less well understood. In the present study, we provide evidence that the conserved microRNA miR-210 regulates lipid metabolism and prevents neurodegeneration in the Drosophila retina. miR-210 is specifically expressed in the photoreceptor neurons and other sensory organs. Genetic deletion of miR-210 leads to lipid droplet accumulation and photoreceptor degeneration in the retina. These effects are associated with abnormal activation of the Drosophila sterol regulatory element-binding protein signaling. We further identify the acetyl-coenzyme A synthetase (ACS) as one functionally important target of miR-210 in this context. Reduction of ACS in the miR-210 mutant background suppresses the neurodegeneration defects, suggesting that miR-210 acts through regulation of the ACS transcript. Together, these results reveal an unexpected role of miR-210 in controlling lipid metabolism and neuronal functions.

Better Sleep at Night: How Light Influences Sleep in Drosophila

Sleep-like states have been described in Drosophila and the mechanisms and factors that generate and define sleep-wake profiles in this model organism are being thoroughly investigated. Sleep is controlled by both circadian and homeostatic mechanisms, and environmental factors such as light, temperature, and social stimuli are fundamental in shaping and confining sleep episodes into the correct time of the day. Among environmental cues, light seems to have a prominent function in modulating the timing of sleep during the 24 h and, in this review, we will discuss the role of light inputs in modulating the distribution of the fly sleep-wake cycles. This phenomenon is of growing interest in the modern society, where artificial light exposure during the night is a common trait, opening the possibility to study Drosophila as a model organism for investigating shift-work disorders.

MicroRNA: A Key Player for the Interplay of Circadian Rhythm Abnormalities, Sleep Disorders and Neurodegenerative Diseases

Circadian rhythms are endogenous 24-h oscillators that regulate the sleep/wake cycles and the timing of biological systems to optimize physiology and behavior for the environmental day/night cycles. The systems are basically generated by transcription-translation feedback loops combined with post-transcriptional and post-translational modification. Recently, evidence is emerging that additional non-coding RNA-based mechanisms are also required to maintain proper clock function. MicroRNA is an especially important factor that plays critical roles in regulating circadian rhythm as well as many other physiological functions. Circadian misalignment not only disturbs the sleep/wake cycle and rhythmic physiological activity but also contributes to the development of various diseases, such as sleep disorders and neurodegenerative diseases. The patient with neurodegenerative diseases often experiences profound disruptions in their circadian rhythms and/or sleep/wake cycles. In addition, a growing body of recent evidence implicates sleep disorders as an early symptom of neurodegenerative diseases, and also suggests that abnormalities in the circadian system lead to the onset and expression of neurodegenerative diseases. The genetic mutations which cause the pathogenesis of familial neurodegenerative diseases have been well studied; however, with the exception of Huntington's disease, the majority of neurodegenerative diseases are sporadic. Interestingly, the dysfunction of microRNA is increasingly recognized as a cause of sporadic neurodegenerative diseases through the deregulated genes related to the pathogenesis of neurodegenerative disease, some of which are the causative genes of familial neurodegenerative diseases. Here we review the interplay of circadian rhythm disruption, sleep disorders and neurodegenerative disease, and its relation to microRNA, a key regulator of cellular processes.

miR-263b Controls Circadian Behavior and the Structural Plasticity of Pacemaker Neurons by Regulating the LIM-Only Protein Beadex

: Circadian clocks drive rhythmic physiology and behavior to allow adaption to daily environmental changes. In Drosophila, the small ventral lateral neurons (sLNvs) are primary pacemakers that control circadian rhythms. Circadian changes are observed in the dorsal axonal projections of the sLNvs, but their physiological importance and the underlying mechanism are unclear. Here, we identified miR-263b as an important regulator of circadian rhythms and structural plasticity of sLNvs in Drosophila. Depletion of miR-263b (miR-263b^KO) in flies dramatically impaired locomotor rhythms under constant darkness. Indeed, miR-263b is required for the structural plasticity of sLNvs. miR-263b regulates circadian rhythms through inhibition of expression of the LIM-only protein Beadex (Bx). Consistently, overexpression of Bx or loss-of-function mutation (Bx^hdpR26) phenocopied miR-263b^KO and miR-263b overexpression in behavior and molecular characteristics. In addition, mutating the miR-263b binding sites in the Bx 3' UTR using CRISPR/Cas9 recapitulated the circadian phenotypes of miR-263b^KO flies. Together, these results establish miR-263b as an important regulator of circadian locomotor behavior and structural plasticity.