A species-specific miRNA participates in biomineralization by targeting CDS regions of Prisilkin-39 and ACCBP in Pinctada fucata

The accumulation of modular serine protease mediated by a novel circRNA sponging miRNA increases Aedes aegypti immunity to fungus

BACKGROUND

Mosquitoes transmit many infectious diseases that affect human health. The fungus Beauveria bassiana is a biological pesticide that is pathogenic to mosquitoes but harmless to the environment.

RESULTS

We found a microRNA (miRNA) that can modulate the antifungal immunity of Aedes aegypti by inhibiting its cognate serine protease. Fungal infection can induce the expression of modular serine protease (ModSP), and ModSP knockdown mosquitoes were more sensitive to B. bassiana infection. The novel miRNA-novel-53 is linked to antifungal immune response and was greatly diminished in infected mosquitoes. The miRNA-novel-53 could bind to the coding sequences of ModSP and impede its expression. Double fluorescence in situ hybridization (FISH) showed that this inhibition occurred in the cytoplasm. The amount of miRNA-novel-53 increased after miRNA agomir injection. This resulted in a significant decrease in ModSP transcript and a significant increase in mortality after fungal infection. An opposite effect was produced after antagomir injection. The miRNA-novel-53 was also knocked out using CRISPR-Cas9, which increased mosquito resistance to the fungus B. bassiana. Moreover, mosquito novel-circ-930 can affect ModSP mRNA by interacting with miRNA-novel-53 during transfection with siRNA or overexpression plasmid.

CONCLUSIONS

Novel-circ-930 affects the expression level of ModSP by a novel-circ-930/miRNA-novel-53/ModSP mechanism to modulate antifungal immunity, revealing new information on innate immunity in insects.

Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas

The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.

Immunomodulatory effects of one novel microRNA miR-63 in pearl oyster Pinctada fucata martensii

Novel microRNA miR-63 (novel-miR-63) from pearl oyster Pinctada fucata martensii (Pm-novel-miR-63) is a species-specific miRNA. Our previous research has shown that the expression of Pm-novel-miR-63 was significantly downregulated at 24 h after nucleus transplantation. In this study, we analyzed the function and regulatory role of Pm-novel-miR-63 in the immune response of pearl oysters. The results showed that Pm-novel-miR-63 expression increased after the stimulation of pathogen associated molecular patterns at 6-12 h, and the activity of immune and antioxidant enzymes in the serum decreased after Pm-novel-miR-63 overexpression. Transcriptome analysis revealed that Pm-novel-miR-63 participated in regulating transplantation immunity through the Notch and mRNA surveillance signaling pathways. Target prediction and dual luciferase analysis revealed that Pm-GDP-FucTP, Pm-CysLTR2, and Pm-RLR were the target genes of Pm-novel-miR-63. These results suggested that Pm-novel-miR-63 participated in regulating the immune response in pearl oysters and can serve as a new interference target to reasonably control excessive immune rejection in pearl culture.

Identification of Species-Specific MicroRNAs Provides Insights into Dynamic Evolution of MicroRNAs in Plants

MicroRNAs (miRNAs) are an important class of regulatory small RNAs that program gene expression, mainly at the post-transcriptional level. Although sporadic examples of species-specific miRNAs (termed SS-miRNAs) have been reported, a genome-scale study across a variety of distant species has not been assessed. Here, by comprehensively analyzing miRNAs in 81 plant species phylogenetically ranging from chlorophytes to angiosperms, we identified 8048 species-specific miRNAs from 5499 families, representing over 61.2% of the miRNA families in the examined species. An analysis of the conservation from different taxonomic levels supported the high turnover rate of SS-miRNAs, even over short evolutionary distances. A comparison of the intrinsic features between SS-miRNAs and NSS-miRNAs (non-species-specific miRNAs) indicated that the AU content of mature miRNAs was the most striking difference. Our data further illustrated a significant bias of the genomic coordinates towards SS-miRNAs lying close to or within genes. By analyzing the 125,267 putative target genes for the 7966 miRNAs, we found the preferentially regulated functions of SS-miRNAs related to diverse metabolic processes. Collectively, these findings underscore the dynamic evolution of miRNAs in the species-specific lineages.

Plant responses to metals stress: microRNAs in focus

Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.

MicroRNA expression signature in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis

Increasing evidences point to the potential role of microRNAs (miRNAs) in muscle growth and development in animals. However, knowledge on the identity of miRNAs and their targets in molluscs remains largely unknown. Scallops have one large adductor muscle, composed of fast (striated) and slow (smooth) muscle types, which display great differences in muscle fibers, meat quality, cell types and molecular components. In the present study, we performed a comprehensive investigation of miRNA transcriptomes in fast and slow adductor muscles of Yesso scallop Patinopecten yessoensis. As a result, 47 differentially expressed miRNAs representing ten miRNA families were identified between the striated and smooth adductor muscles. The KEGG enrichment analysis of their target genes were mainly associated with amino acid metabolism, energy metabolism and glycan biosynthesis. The target genes of miR-133 and miR-71 were validated by the dual-luciferase reporter assays and miRNA antagomir treatment in vivo. The identification and functional validation of these different miRNAs in scallops will greatly help our understanding of miRNA regulatory mechanism that achieves the unique muscle phenotypes in scallops. The present findings provide the direct evidences for muscle-specific miRNAs involved in muscle growth and differentiation in molluscs.

Integration detection of mercury(ii) and GSH with a fluorescent "on-off-on" switch sensor based on nitrogen, sulfur co-doped carbon dots

Using aurine and citric acid as precursors, we have synthesized stable blue-fluorescent nitrogen and sulfur co-doped carbon dots (NS-CDs), with a high quantum yield of up to 68.94% via a thermal lysis method. The fluorescent NS-CDs were employed as a sensitive sensor for the integration detection of Hg2+ and glutathione (GSH). This was attributed to Hg2+ effectively quenching the fluorescence of the NS-CDs by static quenching, and then GSH was able to recover the fluorescence owing to the stronger binding between Hg2+ and the sulfhydryl of GSH. Based on the "on-off-on" tactic, the detection limits of Hg2+ ions and GSH were 50 nM and 67 nM respectively. The fluorescence sensor was successfully applied to detect Hg2+ ions and GSH in actual samples (tap water and fetal bovine serum). Furthermore, we have proved that the sensor had good reversibility. Overall, our NS-CDs can serve as effective sensors for environmental and biological analysis in the future.

Primate-specific retrotransposons and the evolution of circadian networks in the human brain

The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.

MiR-205 is up-regulated in islets of diabetes-susceptible mice and targets the diabetes gene Tcf7l2

AIM

MicroRNAs play an important role in the maintenance of cellular functions by fine-tuning gene expression levels. The aim of the current study was to identify genetically caused changes in microRNA expression which associate with islet dysfunction in diabetic mice.

METHODS

To identify novel microRNAs involved in islet dysfunction, transcriptome and miRNome analyses were performed in islets of obese, diabetes-susceptible NZO and diabetes-resistant B6-ob/ob mice and results combined with quantitative trait loci (QTL) and functional in vitro analysis.

RESULTS

In islets of NZO and B6-ob/ob mice, 94 differentially expressed microRNAs were detected, of which 11 are located in diabetes QTL. Focusing on conserved microRNAs exhibiting the strongest expression difference and which have not been linked to islet function, miR-205-5p was selected for further analysis. According to transcriptome data and target prediction analyses, miR-205-5p affects genes involved in Wnt and calcium signalling as well as insulin secretion. Over-expression of miR-205-5p in the insulinoma cell line INS-1 increased insulin expression, left-shifted the glucose-dependence of insulin secretion and supressed the expression of the diabetes gene TCF7L2. The interaction between miR-205-5p and TCF7L2 was confirmed by luciferase reporter assay.

CONCLUSION

MiR-205-5p was identified as relevant microRNA involved in islet dysfunction by interacting with TCF7L2.

Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas)

Molluscan shell color polymorphism is important in genetic breeding, while the molecular information mechanism for shell coloring is unclear. Here, high-throughput RNA sequencing was used to compare expression profiles of coding and non-coding RNAs (ncRNAs) from Pacific oyster Crassostrea gigas with orange and black shell, which were from an F2 family constructed by crossing an orange shell male with a black shell female. First, 458, 13, and 8 differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. Functional analysis suggested that the DEGs were significantly enriched in 9 pathways including tyrosine metabolism and oxidative phosphorylation pathways. Several genes related to melanin synthesis and biomineralization expressed higher whereas genes associated with carotenoid pigmentation or metabolism expressed lower in orange shell oyster. Then, based on the ncRNA analysis, 163 and 20 genes were targeted by 13 and 8 differentially expressed lncRNAs (DELs) and miRNAs (DEMs), severally. Potential DELs-DEMs-DEGs interactions were also examined. Seven DEMs-DEGs pairs were detected, in which tyrosinase-like protein 1 was targeted by lgi-miR-133-3p and lgi-miR-252a and cytochrome P450 was targeted by dme-miRNA-1-3p. These results revealed that melanin synthesis-related genes and miRNAs-mRNA interactions functioned on orange shell coloration, which shed light on the molecular regulation of shell coloration in marine shellfish.

Digging into bivalve miRNAomes: between conservation and innovation

Bivalves are a diverse mollusc group of economic and ecological importance. An evident resilience to pollution, parasites and extreme environments makes some bivalve species important models for studying adaptation and immunity. Despite substantial progress in sequencing projects of bivalves, information on non-coding genes and gene-regulatory aspects is still lacking. Here, we review the current repertoire of bivalve microRNAs (miRNAs), important regulators of gene expression in Metazoa. We exploited available short non-coding RNA (sncRNA) data for Pinctada martensii, Crassostrea gigas, Corbicula fluminea, Tegillarca granosa and Ruditapes philippinarum, and we produced new sncRNA data for two additional bivalves, the Mediterranean mussel Mytilus galloprovincialis and the blood clam Scapharca broughtonii. We found substantial heterogeneity and incorrect annotations of miRNAs; hence, we reannotated conserved miRNA families using recently established criteria for bona fide microRNA annotation. We found 106 miRNA families missing in the previously published bivalve datasets and 89 and 87 miRNA complements were identified in the two additional species. The overall results provide a homogeneous and evolutionarily consistent picture of miRNAs in bivalves and enable future comparative studies. The identification of two bivalve-specific miRNA families sheds further light on the complexity of transcription and its regulation in bivalve molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.

The functional roles of the non-coding RNAs in molluscs

This review focus on the current knowledge of non-coding RNAs (ncRNAs) in molluscs. In this review, we provide an overview of long ncRNAs (lncRNA), microRNAs (miRNA) and piwi-interacting RNAs (piRNA), followed by evidence for the regulation of ncRNAs in variety of biological process in molluscs, including development, biomineralization and innate immune response. This review advances our understanding on the roles of ncRNAs in molluscs and suggest the future direction to fully understand the epigenetic regulatory network of molluscs.