Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation

Cardiac microRNA expression profile in response to estivation

Couch's spadefoot toad (Scaphiopus couchii) spends most of the year underground in a hypometabolic state known as estivation. During this time, they overcome significant dehydration and lack of food through many mechanisms including employing metabolic rate depression (MRD), increasing urea concentration, switching to lipid oxidation as the primary energy source, and decreasing their breathing and heart rate. MicroRNA (miRNA) are known to regulate translation by targeting messenger RNA (mRNA) for degradation or temporary storage, with several studies having reported that miRNA is differentially expressed during MRD, including estivation. Thus, we hypothesized that miRNA would be involved in gene regulation during estivation in S. couchii heart. Next-generation sequencing and bioinformatic analyses were used to assess changes in miRNA expression in response to two-month estivation and to predict the downstream effects of this expression. KEGG and GO analyses indicated that ribosome and cardiac muscle contraction are among the pathways predicted to be upregulated, whereas cell signaling and fatty acid metabolism were predicted to be downregulated. Together these results suggest that miRNAs contribute to the regulation of gene expression related to cardiac muscle physiology and energy metabolism during estivation.

Role of MicroRNAs in Extreme Animal Survival Strategies

The critical role microRNAs play in modulating global functions is emerging, both in the maintenance of homeostatic mechanisms and in the adaptation to diverse environmental stresses. When stressed, cells must divert metabolic requirements toward immediate survival and eventual recovery and the unique features of miRNAs, such as their relatively ATP-inexpensive biogenesis costs, and the quick and reversible nature of their action, renders them excellent "master controllers" for rapid responses. Many animal survival strategies for dealing with extreme environmental pressures involve prolonged retreats into states of suspended animation to extend the time that they can survive on their limited internal fuel reserves until conditions improve. The ability to retreat into such hypometabolic states is only possible by coupling the global suppression of nonessential energy-expensive functions with an activation of prosurvival networks, a process in which miRNAs are now known to play a major role. In this chapter, we discuss the activation, expression, biogenesis, and unique attributes of miRNA regulation required to facilitate profound metabolic rate depression and implement stress-specific metabolic adaptations. We examine the role of miRNA in strategies of biochemical adaptation including mammalian hibernation, freeze tolerance, freeze avoidance, anoxia and hypoxia survival, estivation, and dehydration tolerance. By comparing these seemingly different adaptive programs in traditional and exotic animal models, we highlight both unique and conserved miRNA-meditated mechanisms for survival. Additional topics discussed include transcription factor networks, temperature dependent miRNA-targeting, and novel species-specific and stress-specific miRNAs.

Clustering genomic organization of sea cucumber miRNAs impacts their evolution and expression

Echinoderms are marine deuterostomes with fascinating adaptation features such as aestivation and organ regeneration. However, post-transcriptional gene regulation by microRNAs (miRNAs) underlying these features are largely unexplored. Here, using homology-based and de novo approaches supported by expression data, we provided a comprehensive annotation of miRNA genes in the sea cucumber Apostichopus japonicus. By linkage and phylogenic analyses, we characterized miRNA genomic organization, evolutionary history and expression regulation. The results showed that sea cucumbers evolved a large number of new miRNAs, which tended to form polycistronic clusters via tandem duplication that had been especially active in the echinoderms. Most new miRNAs were weakly expressed, but miRNA clustering increased the expression level of clustered new miRNAs. The most abundantly expressed new miRNAs were organized in a single tandem cluster (cluster n2), which was activated during aestivation and intestine regeneration. Overall, our analyses suggest that clustering of miRNAs is important for their evolutionary origin, expression control, and functional cooperation.

Stress responses in expressions of microRNAs in mussel Mytilus galloprovincialis exposed to cadmium

MicroRNAs (miRNAs) are known to have complicated functions in aquatic species, but little is known about the role of miRNAs in mollusk species under environmental stress. In this study, we performed small RNA sequencing to characterize the differentially expressed miRNAs in different tissues (whole tissues, digestive glands, gills, and gonads) of blue mussels (Mytilus galloprovincialis) exposed to cadmium (Cd). In summary, 107 known miRNAs and 32 novel miRNAs were significantly (p < 0.01) differentially expressed after Cd exposure. The peak size of miRNAs was 22 nucleotides. Target genes of these differentially expressions of miRNAs related to immune defense, apoptosis, lipid and xenobiotic metabolism showed significant changes under Cd stress. These findings provide the first characterization of miRNAs in mussel M. galloprovincialis and expressions of many target genes in response to Cd stress.

Insights into the DNA methylation of sea cucumber Apostichopus japonicus in response to skin ulceration syndrome infection

DNA methylation is an important epigenetic modification that regulates gene expression in many biological processes, including immune response. In this study, whole-genome bisulfite sequencing (WGBS) was carried out on healthy body wall (HB) and skin ulceration syndrome (SUS) infected body wall (SFB) to gain insights into the epigenetic regulatory mechanism in sea cucumber Apostichopus japonicus. After comparison, a total of 116,522 differentially methylated regions (DMRs) were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs (p < 0.05, FDR < 0.001). GO enrichment analysis indicated that regulation of DNA-templated transcription (GO: 0006355), where DNA methylation occurred, was the most significant term in the biology process. The integration of methylome and transcriptome analysis revealed that 10,499 DMRs were negatively correlated with 496 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were enriched in the phosphoinositide 3-kinase-protein kinase B (PI3K/Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Interestingly, two serine/threonine-protein kinases, nemo-like kinase (NLK) and mTOR, were highlighted after functional analysis. The variations of methylation in these two genes were associated with SUS infection and immune regulation. They regulated gene expression at different levels and showed interaction during response process. The validation of methylation sites showed high consistency between pyrosequencing and WGBS. WGBS analysis not only revealed the changes of DNA methylation, but also presented important information about the regulation of key genes after SUS infection in A. japonicus.

The OxymiR response to oxygen limitation: a comparative microRNA perspective

From squid at the bottom of the ocean to humans at the top of mountains, animals have adapted to diverse oxygen-limited environments. Surviving these challenging conditions requires global metabolic reorganization that is orchestrated, in part, by microRNAs that can rapidly and reversibly target all biological functions. Herein, we review the involvement of microRNAs in natural models of anoxia and hypoxia tolerance, with a focus on the involvement of oxygen-responsive microRNAs (OxymiRs) in coordinating the metabolic rate depression that allows animals to tolerate reduced oxygen levels. We begin by discussing animals that experience acute or chronic periods of oxygen deprivation at the ocean's oxygen minimum zone and go on to consider more elevated environments, up to mountain plateaus over 3500 m above sea level. We highlight the commonalities and differences between OxymiR responses of over 20 diverse animal species, including invertebrates and vertebrates. This is followed by a discussion of the OxymiR adaptations, and maladaptations, present in hypoxic high-altitude environments where animals, including humans, do not enter hypometabolic states in response to hypoxia. Comparing the OxymiR responses of evolutionarily disparate animals from diverse environments allows us to identify species-specific and convergent microRNA responses, such as miR-210 regulation. However, it also sheds light on the lack of a single unified response to oxygen limitation. Characterizing OxymiRs will help us to understand their protective roles and raises the question of whether they can be exploited to alleviate the pathogenesis of ischemic insults and boost recovery. This Review takes a comparative approach to addressing such possibilities.

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.

Functional impact of microRNA regulation in models of extreme stress adaptation

When confronted with severe environmental stress, some animals are able to undergo a substantial reorganization of their cellular environment that enables long-term survival. One molecular mechanism of adaptation that has received considerable attention in recent years has been the action of reversible transcriptome regulation by microRNA. The implementation of new computational and high-throughput experimental approaches has started to uncover the vital contributions of microRNA towards stress adaptation. Indeed, recent studies have suggested that microRNA may have a major regulatory influence over a number of cellular processes that are essential to prolonged environmental stress survival. To date, a number of studies have highlighted the role of microRNA in the regulation of a metabolically depressed state, documenting stress-responsive microRNA expression during mammalian hibernation, frog and insect freeze tolerance, and turtle and marine snail anoxia tolerance. These studies collectively indicate a conserved principle of microRNA stress response across phylogeny. As we are on the verge of dissecting the role of microRNA in environmental stress adaptation, this review summarizes recent research advances and the hallmark expression patterns that facilitate stress survival.

MiR-200-3p Is Potentially Involved in Cell Cycle Arrest by Regulating Cyclin A during Aestivation in Apostichopus japonicus

The sea cucumber (Apostichopus japonicus) has become a good model organism for studying environmentally induced aestivation in marine invertebrates. We hypothesized that mechanisms that arrest energy-expensive cell cycle activity would contribute significantly to establishing the hypometabolic state during aestivation. Cyclin A is a core and particularly interesting cell cycle regulator that functions in both the S phase and in mitosis. In the present study, negative relationships between miR-200-3p and AjCA expressions were detected at both the transcriptional and the translational levels during aestivation in A. japonicus. Dual-luciferase reporter assays confirmed the targeted location of the miR-200-3p binding site within the AjCA gene transcript. Furthermore, gain- and loss-of-function experiments were conducted in vivo with sea cucumbers to verify the interaction between miR-200-3p and AjCA in intestine tissue by qRT-PCR and Western blotting. The results show that the overexpression of miR-200-3p mimics suppressed AjCA transcript levels and translated protein production, whereas transfection with a miR-200-3p inhibitor enhanced both AjCA mRNA and AjCA protein in A. japonicus intestine. Our findings suggested a potential mechanism that reversibly arrests cell cycle progression during aestivation, which may center on miR-200-3p inhibitory control over the translation of cyclin A mRNA transcripts.

Estivation-responsive microRNAs in a hypometabolic terrestrial snail

When faced with extreme environmental conditions, the milk snail (Otala lactea) enters a state of dormancy known as estivation. This is characterized by a strong reduction in metabolic rate to <30% of normal resting rate that is facilitated by various behavioural, physiological, and molecular mechanisms. Herein, we investigated the regulation of microRNA in the induction of estivation. Changes in the expression levels of 75 highly conserved microRNAs were analysed in snail foot muscle, of which 26 were significantly upregulated during estivation compared with controls. These estivation-responsive microRNAs were linked to cell functions that are crucial for long-term survival in a hypometabolic state including anti-apoptosis, cell-cycle arrest, and maintenance of muscle functionality. Several of the microRNA responses by snail foot muscle also characterize hypometabolism in other species and support the existence of a conserved suite of miRNA responses that regulate environmental stress responsive metabolic rate depression across phylogeny.

The potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber

The sea cucumber (Apostichopus japonicus) has become a good model organism for studying environmentally-induced aestivation by a marine invertebrate more recently. In the present study, we hypothesized that miRNA-200-3p may contribute to establish rapid biological control to regulate fatty acid metabolism during a estivation. The peroxisomal bi-functional enzyme (EHHADH) is a crucial participant of the classical peroxisomal fatty acid β-oxidation pathway, the relative mRNA transcripts and protein expressions of EHHADH were analyzed in intestine from sea cucumbers experienced long-term aestivation. Both mRNA transcripts and protein expressions of EHHADH in intestine decreased significantly during deep-aestivation as compared with non-aestivation controls. Analysis of the 3′ UTR of AjEHHADH showed the presence of a conserved binding site for miR-200-3p. Level of miR-200-3p showed an inverse correlation with EHHADH mRNA transcripts and protein levels in intestine, implicating miR-200-3p may directly targeted AjEHHADH by inducing the degradation of AjEHHADH mRNA in the aestivating sea cucumber, further dual-luciferase reporter assay validated the predicted role of miRNA-200-3p in regulating AjEHHADH. In order to further understand their regulatory mechanism, we conducted the functional experiment in vivo. The overexpression of miR-200-3p in sea cucumber significantly decreased mRNA and protein expression levels of AjEHHADH. Taken together, these findings suggested the potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber.

Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: Essential regulators in the heat stress-host interactions

Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions. In the present study, miRNAs with heat stress responsive and immune properties were identified and characterized in M. japonicus by small RNA sequencing and bioinformatics analysis. In total, 79 host miRNAs were identified, among which 15 miRNAs were differentially expressed in response to heat stress. Target genes prediction and function annotation revealed that a variety of host cellular processes, such as signal transduction, transcription, anti-stress response, ribosomal biogenesis, lipid metabolism, cytoskeleton, etc, were potentially subject to miRNA-mediated regulation in response to heat stress. Furthermore, a total of 30 host miRNAs that potentially involved in interaction with white spot syndrome virus (WSSV) were obtained via predicting and analyzing the target genes from WSSV. The results showed that a batch of WSSV genes that code for structural proteins and enzymes that are essential for WSSV infection and proliferation, such as envelope proteins, capsid proteins, immediate-early proteins, collagen-like protein, protein kinase, thymidylate synthetase, TATA-box bind protein, etc, were predicted to be targeted by host miRNAs. Several of the host miRNAs with predicted antiviral capacity were down-regulated under heat stress, indicating a repression of host miRNA-mediated antiviral immune response. This study highlighted the essential roles of host miRNAs in the heat stress-host interactions and provided valuable information for further investigation on the mechanism of miRNA-mediated heat stress and immune response of shrimp.

Micromanaging freeze tolerance: the biogenesis and regulation of neuroprotective microRNAs in frozen brains

When temperatures plummet below 0 °C, wood frogs (Rana sylvatica) can endure the freezing of up to ~ 65% of their body water in extracellular ice masses, displaying no measurable brain activity, no breathing, no movement, and a flat-lined heart. To aid survival, frogs retreat into a state of suspended animation characterized by global suppression of metabolic functions and reprioritization of energy usage to essential survival processes that is elicited, in part, by the regulatory controls of microRNAs. The present study is the first to investigate miRNA biogenesis and regulation in the brain of a freeze tolerant vertebrate. Indeed, proper brain function and adaptations to environmental stimuli play a crucial role in coordinating stress responses. Immunoblotting of miRNA biogenesis factors illustrated an overall reduction in the majority of these processing proteins suggesting a potential suppression of miRNA maturation over the freeze-thaw cycle. This was coupled with a large-scale RT-qPCR analysis of relative expression levels of 113 microRNA species in the brains of control, 24 h frozen, and 8 h thawed R. sylvatica. Of the 41 microRNAs differentially regulated during freezing and thawing, only two were significantly upregulated. Bioinformatic target enrichment of the downregulated miRNAs, performed at the low temperatures experienced during freezing and thawing, predicted their involvement in the potential activation of various neuroprotective processes such as synaptic signaling, intracellular signal transduction, and anoxia/ischemia injury protection. The predominantly downregulated microRNA fingerprint identified herein suggests a microRNA-mediated cryoprotective mechanism responsible for maintaining neuronal functions and facilitating successful whole brain freezing and thawing.

In-depth profiling of miRNA regulation in the body wall of sea cucumber Apostichopus japonicus during skin ulceration syndrome progression

MicroRNAs (miRNAs) are small non-coding RNAs that mediate mRNA degradation or translation repression. Previous study showed that the expression of miRNAs was significantly changed in the body wall of sea cucumber Apostichopus japonicus after skin ulceration syndrome (SUS) infection, which is a dynamic process. However, the critical miRNAs from body wall that involved in different infection stages of SUS remain unknown. In this study, four cDNA libraries were constructed with the body wall from healthy and three SUS-infected stages of A. japonicus. A total of 248 conserved miRNAs and five novel miRNAs were identified through Illumina HiSeq 2000 platform. Compared to the control, 238 miRNAs showed significant differential expression at three stages of SUS progression. Totally, 3149 miRNA-mRNA pairs were identified by target prediction and 314 miRNA-mRNA pairs showed negative correlation. It is noteworthy that 15 miRNAs and four mRNAs were located at the crucial positions of the network built with the anti-correlated miRNA-mRNA pairs. GO and KEGG enrichment analysis indicated that the predicted targets were involved in many immune-related processes. Deep analysis of miR-31c-5p, miR-29b-3p, NF-kB, mucin 2 and titin showed that they may play important roles in the pathogens attachment and recognition, signaling transduction and lesions repair of A. japonicus after SUS infection. These results would be useful for further investigating the potential roles of critical miRNAs and mRNAs in A. japonicus immune regulation.

A potential antiapoptotic regulation: The interaction of heat shock protein 70 and apoptosis-inducing factor mitochondrial 1 during heat stress and aestivation in sea cucumber

The sea cucumber (Apostichopus japonicus) has become a good model organism for studying environmentally induced aestivation in marine invertebrates. A characteristic feature of aestivation in this species is the degeneration of the intestine. In the current study, we hypothesized that energy conservation and cytoprotective strategies need to be coordinated in the intestine to ensure long-term survival during aestivation, and there was potential relationship between heat shock protein 70 (HSP70) and apoptosis-inducing factor mitochondrial 1 (AIFM1) during extreme environmental stress. AIFM1 is a bifunctional flavoprotein that is involved in the caspase-independent activation of apoptosis. The gene and protein expression profiles of AjAIFM1 and AjHSP70 in intestinal tissue during aestivation were analyzed and results showed an inverse correlation between them, AjAIFM1 being suppressed during aestivation whereas AjHSP70 was strongly upregulated. Comparable responses were also seen when intestinal cells were isolated and analyzed in vitro for responses to heat stress at 25°C (a water temperature typical during aestivation), compared with 15°C control cells. Combined with co-immunoprecipitation studies in vivo and in vitro, our results suggested that AjHSP70 protein may have potential interaction with AjAIFM1. To determine the influence of heat stress on apoptotic rate of intestinal cells, we also assessed the DNA fragmentation by terminal deoxynucleotide transferase-mediated dUTP nick-end labeling assay, and results also supported a potential antiapoptotic response in sea cucumber during heat stress. This type of cytoprotective mechanism could be used to preserve the existing cellular components during long-term aestivation in sea cucumber.

Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress

MicroRNAs (miRNAs) are small noncoding RNAs that regulate diverse cellular processes, including organismal stress response, through posttranscriptional repression of gene transcripts. They are known to have antiviral functions in aquatic crustacean species, but little is known about the role of miRNAs against environmental stress caused by Cu, a common chemical contaminant in aquatic environment. We performed small RNA sequencing to characterize the differentially expressed microRNAs in Cu exposed shrimp. A total of 4524 known miRNAs and 73 novel miRNAs were significantly (P < .05) differentially expressed after Cu exposure. The peak size of miRNAs was 22 nt. Among them, 218 miRNAs were conserved across 115 species. The validation of 12 miRNAs by stem-loop quantitative RT-PCR were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.707). Target genes of these differentially expressed miRNAs related to immune defense, apoptosis, and xenobiotics metabolism also showed significant changes in expression under Cu stress. The present study provides the first characterization of L. vannamei miRNAs and some target genes expression in response to Cu stress, and the findings support the hypothesis that certain miRNAs along with their target genes might be essential in the intricate adaptive response regulation networks. Our current study will provide valuable information to take an insight into molecular mechanism of L. vannamei against environmental stress.

Small noncoding RNA expression during extreme anoxia tolerance of annual killifish (Austrofundulus limnaeus) embryos

Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days at their peak tolerance at 25°C. Their anoxia tolerance and physiology vary over development, such that both anoxia-tolerant and anoxia-sensitive phenotypes comprise the species. This allows for a robust comparison to identify sncRNAs essential to anoxia-tolerance. For this study, RNA sequencing was used to identify and quantify expression of sncRNAs in four embryonic stages of A. limnaeus in response to an exposure to anoxia and subsequent aerobic recovery. Unique stage-specific patterns of expression were identified that correlate with anoxia tolerance. In addition, embryos of A. limnaeus appear to constitutively express stress-responsive miRNAs. Most differentially expressed sncRNAs were expressed at higher levels during recovery. Many novel groups of sncRNAs with expression profiles suggesting a key role in anoxia tolerance were identified, including sncRNAs derived from mitochondrial tRNAs. This global analysis has revealed groups of candidate sncRNAs that we hypothesize support anoxia tolerance.

miR-338-3p inhibits the invasion of renal cell carcinoma by downregulation of ALK5

Background

The current study aims to elucidate the role of miRNA-338-3p (miR-338-3p) in the invasion of renal cell carcinoma (RCC).

Methods

Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to detect the expression of miR-338-3p in human RCC cell lines with high metastatic potential (Caki-1) and low metastatic potential (786-O), respectively. The Caki-1 and 786-O cells were transfected with miR-338-3p mimic or inhibitor. Wound healing assay, Transwell assay and western blotting were performed to analyze the invasive ability and expression of activin receptor-like kinase 5 (ALK5) in the RCC cell lines. During the 36-month follow-up, we detected the expressions of miR-338-3p and ALK5 in 22 RCC cases with metastasis and 60 cases achieving a remission.

Results

miR-339-3p was significantly downregulated in the Caki-1 cells as compared with the 786-O cells. The transfection with miR-338-3p inhibitor caused an increased invasive ability of both two cell lines. However, the transfection with miR-338-3p mimic caused a reduction of the invasiveness. In RCC cells, the expression of ALK5 was negatively correlated to miR-338-3p. Upregulation of ALK5 partially counteracted the miR-338-3p-induced invasiveness of RCC cells. We subsequently found the negative correlations between miR-338-3p and metastasis/ALK5 expression could be also observed in human RCC tissues.

Conclusion

Taken together, these results indicate that miR-338-3p acts as a novel tumor suppressor to inhibit the invasion of RCC by regulating ALK5 expression.

Stress-responsive microRNAs are involved in re-programming of metabolic functions in hibernators

Mammalian hibernation includes re-programing of metabolic capacities, partially, encouraged by microRNAs (miRNAs). Albeit much is known about the functions of miRNAs, we need learning on low temperature miRNAs target determination. As hibernators can withstand low body temperatures (TB) for a long time without anguish tissue damage, understanding the means and mechanisms that empower them to do as such are of restorative intrigue. Nonetheless, these mechanisms by which miRNAs and the hibernators react to stressful conditions are not much clear. It is evident from recent data that the gene expression and the translation of mRNA to protein are controlled by miRNAs. The miRNAs also influence regulation of major cellular processes. As the significance of miRNAs in stress conditions adaptation are getting clearer, this audit article abridges the key alterations in miRNA expression and the mechanism that facilitates stress survival.

MicroRNA Stability in FFPE Tissue Samples: Dependence on GC Content

MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88 <r < 0.92). However, the relative read count of each miRNA was different depending on the GC content (p<0.0001). The unequal degradation of each miRNA affected the abundance ranking in the library, and miR-133a was shown to be the most abundant in FFPE cardiac tissues instead of miR-1, which was predominant before fixation. Subsequent quantitative PCR (qPCR) analyses revealed that miRNAs with GC content of less than 40% are more degraded than GC-rich miRNAs (p<0.0001). We showed that deep sequencing data obtained using FFPE samples cannot be directly compared with that of fresh frozen samples. The combination of miRNA deep sequencing and other quantitative analyses, such as qPCR, may improve the utility of archival FFPE tissue samples.

Gene structure, expression, and DNA methylation characteristics of sea cucumber cyclin B gene during aestivation

The sea cucumber, Apostichopus japonicus, is a good model for studying environmentally-induced aestivation by a marine invertebrate. One of the central requirements of aestivation is the repression of energy-expensive cellular processes such as cell cycle progression. The present study identified the gene structure of the cell cycle regulator, cyclin B, and detected the expression levels of this gene over three stages of the annual aestivation-arousal cycle. Furthermore, the DNA methylation characteristics of cyclin B were analyzed in non-aestivation and deep-aestivation stages of sea cucumbers. We found that the cyclin B promoter contains a CpG island, three CCAAT-boxes and three cell cycle gene homology regions (CHRs). Application of qRT-PCR analysis showed significant downregulation of cyclin B transcript levels during deep-aestivation in comparison with non-aestivation in both intestine and longitudinal muscle, and these returned to basal levels after arousal from aestivation. Methylation analysis of the cyclin B core promoter revealed that its methylation level showed significant differences between non-aestivation and deep-aestivation stages (p<0.05) and interestingly, a positive correlation between Cyclin B transcripts expression and methylation levels of the core promoter was also observed. Our findings suggest that cell cycle progression may be reversibly arrested during aestivation as indicated by the changes in cyclin B expression levels and we propose that DNA methylation is one of the regulatory mechanisms involved in cyclin B transcriptional variation.

Expression analysis of microRNAs related to the skin ulceration syndrome of sea cucumber Apostichopus japonicus

MicroRNAs (miRNAs) are small non-coding RNAs that are involved in many biological processes. To investigate the miRNAs related to skin ulceration syndrome (SUS) of Apostichopus japonicus, small RNA libraries of body wall, intestine, respiratory tree and coelomocytes from healthy and diseased A. japonicus were sequenced on Illumina Hiseq 2000 platform. A total of 247 conserved and 10 novel miRNAs were identified across all libraries. After pair-wise comparisons, 215 miRNAs in body wall, 36 in intestine, 2 in respiratory tree and 38 in coelomocytes showed significant expression differences. Further analyses were conducted on some tissue-specific differentially expressed miRNAs: miR-8 and miR-486-5p in body wall, miR-200-3p, let-7-5p and miR-125 in intestine, miR-278a-3p and bantam in respiratory, miR-10a and miR-184 in coelomocytes. Notably, these miRNAs in some species were reported to function in various physiological or pathological processes associated with immune regulations. Using stem-loop quantitative real time PCR, six representative miRNAs in four tissues were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the six miRNAs ranged from 0.777 to 0.948, which confirmed the consistency and accuracy between these two approaches. This study provides comprehensive expression and regulation patterns of functional miRNAs in different tissues and gives insights into the tissue-specific immune response mechanisms in SUS-infected A. japonicus.

Reproducibility of quantitative real-time PCR assay in microRNA expression profiling and comparison with microarray analysis in narcolepsy

MicroRNAs (miRNAs) have been shown in the pathogenesis of human neurological disorders. The study aims to identify the involvement of miRNAs in the pathophysiology of narcolepsy. Here, we conducted three independent high-throughput analysis of miRNA (miRNA microarray) in peripheral blood from 20 narcolepsy patients who fulfilled the criteria compared to 20 healthy controls with validation experiment using quantitative real-time polymerase chain reaction (real-time PCR) panels. By analyzing 2805 miRNAs in peripheral blood with microarray we identified 128 miRNAs (105 high expression and 23 low expression) that were different in patients with narcolepsy in comparison with healthy control. Then we chose six high expression candidates and six low expression candidates of at least twofold difference and p value < 0.05 to validate the changes in three independent experiments in vitro using real-time PCR. The validation test showed that levels of hsa-mir-1267, hsa-miR-4309, hsa-miR-554, hsa-miR-1272, hsa-miR-4501, hsa-miR-182-3p were higher, whereas the level of hsa-miR-625-5p, hsa-miR-100-5p, hsa-miR-125b-5p, hsa-miR-197-3p, hsa-miR-4522, hsa-miR-493-5p was lower in narcolepsy patients than healthy controls. The levels of 12 miRNAs differed significantly in peripheral blood from narcolepsy patients which suggested that alterations of miRNAs expression may be involved in the pathophysiology of narcolepsy.

Identification and comparative analysis of complement C3-associated microRNAs in immune response of Apostichopus japonicus by high-throughput sequencing

MicroRNAs (miRNAs) are important effectors in mediating host–pathogen interaction. In this report, coelomocytes miRNA libraries of three Japanese sea cucumbers Apostichopus japonicus were built by Illumina^® Hiseq2000 from different time points after lipopolysaccharide challenge (at time 0 h, 6 h and 12 h). The clean data received from high throughput sequencing were used to sequences analysis. Referenced to the Strongylocentrotus purpuratus genome, 38 conserved miRNAs were found, and three miRNA candidates were predicted by software. According to the evidence resulting from the expression of AjC3, expressing levels of spu-miR-133, spu-miR-137 and spu-miR-2004 altered along with the expression of AjC3 changing at different time points after LPS injection. Thus, we speculated that the three miRNAs may have influence on A. japonicus complement C3. The spu-miR-137 and miR-137 gene family in miRBase were analyzed by bioinformatics. There is an obvious discrepancy between invertebrates and vertebrates. The first and ninth nucleotides in invertebrate miR-137 are offset compared vertebrate miR-137. Importantly, this is the first attempt to map the stage of immune response regulome in echinoderms, which might be considered as information for elucidating the intrinsic mechanism underlying the immune system in this species.

Comparative phosphoproteomic analysis of intestinal phosphorylated proteins in active versus aestivating sea cucumbers

The sea cucumber Apostichopus japonicus is becoming an excellent model marine invertebrate for studies of environmentally-induced aestivation. Reversible protein phosphorylation as a regulatory mechanism in aestivation is known for some terrestrial aestivators but has never before been documented in sea cucumbers. The present study provides a global quantitative analysis of the role of reversible phosphorylation in sea cucumber aestivation by using tandem mass tag (TMT) labeling followed by an IMAC enrichment strategy to map aestivation-responsive changes in the phosphoproteome of sea cucumber intestine. We identified 2295 unique phosphosites derived from 1283 phosphoproteins and, of these, 211 hyperphosphorylated and 65 hypophosphorylated phosphoproteins were identified in intestine during deep aestivation compared with the active state based on the following criterion: quantitative ratios over 1.5 or less than 0.67 with corrected p-value <0.05. Six major functional classes of proteins exhibited changes in their phosphorylation status during aestivation: (1) protein synthesis, (2) transcriptional regulators, (3) kinases, (4) signaling, (5) transporter, (6) DNA binding. These data on the global involvement of phosphorylation in sea cucumber aestivation significantly improve our understanding of the regulatory mechanisms involved in metabolic arrest when marine invertebrates face environmental stress and provide substantial candidate phosphorylated proteins that could be important for identifying functionally adaptive variation in marine invertebrates.

SIGNIFICANCE

Sea cucumber Apostichopus japonicus is an excellent model organism for studies of environmentally-induced aestivation by a marine invertebrate. The present study provides the first quantitative phosphoproteomic analysis of sea cucumber aestivation using isobaric tag based TMT labeling followed by an IMAC enrichment strategy. These data on the global involvement of phosphorylation in sea cucumber aestivation significantly improve our understanding of the regulatory mechanism involved in metabolic arrest when marine invertebrates face environmental stress and provide substantial candidate phosphorylated proteins that could be important for identifying functionally adaptive variation in marine invertebrates. This study also demonstrates the usefulness of the TMT-based quantitative phosphoproteomics approach to explore the survival responses of a non-model marine invertebrate species to seasonal changes in its environment.

Identification and profiling of miRNAs in the freeze-avoiding gall moth Epiblema scudderiana via next-generation sequencing

The rapid development of high-throughput next-generation sequencing approaches in recent years has facilitated large-scale discovery and expression analysis of non-coding RNAs, including miRNAs, in traditional and non-traditional animal models. Such an approach has been leveraged to amplify, identify, and quantify miRNAs in several models of cold adaptation. The present study is the first to investigate the status of these small RNAs in an insect species that uses the freeze avoidance strategy of cold hardiness, the gall moth Epiblema scudderiana. To characterize the overall miRNA expression profile and to identify cold-modulated miRNAs in control (5 °C) and cold-exposed (-15 °C) E. scudderiana larvae, a next-generation sequencing-based approach was undertaken. A total of 44 differentially expressed miRNAs were identified between the two conditions; 21 up-regulated miRNAs and 23 down-regulated miRNAs in -15 °C-exposed larvae as compared with controls. Among the most significant changes observed in miRNAs with potential relevance to cold adaptation were elevated miR-1-3p, miR-92b-3p, and miR-133-3p levels as well as reduced miR-13a-3p and miR-13b-3p levels in E. scudderiana larvae exposed to cold temperatures. Expression values obtained from next-generation sequencing were also validated by a quantitative PCR approach for five miRNAs; miR-34-5p, miR-274-5p, miR-275-3p, miR-307a-3p, and miR-316-5p. Overall, this work provides the first description of a miRNA signature for subzero survival by a freeze-avoiding insect using a high-throughput approach and positions a new group of miRNAs at the forefront of the molecular changes underlying cold adaptation.

Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing

MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.

Expression of miRNAs in response to freezing and anoxia stresses in the freeze tolerant fly Eurosta solidaginis

Insect cold hardiness is associated with substantial metabolic rate suppression, often including developmental diapause as well as metabolic suppression imposed by freezing and freeze-associated oxygen limitation. MicroRNAs, small non-coding transcripts that bind to mRNA, are known modulators of hypometabolism in freeze tolerant insects. To further contribute to the growing signature of stress-responsive miRNAs, this study amplified and quantified changes in the expression levels of four microRNA species, miR-8, miR-9, miR-92b and miR-277, in response to freezing or anoxia exposures of freeze tolerant gall fly larvae, Eurosta solidaginis. MiR-92b levels were significantly elevated by 1.57-fold in frozen E. solidaginis at -15°C as compared with 5°C controls, whereas miR-92b levels were significantly reduced in anoxic E. solidaginis to levels that were 0.77-fold as compared with larvae held under normoxic conditions. The other miRNAs investigated showed no significant changes in stressed larvae. These data demonstrate differential miR-92b expression in frozen/anoxic versus control insect larvae and position this miRNA as a stress responsive marker in this model insect.

Insight into post-transcriptional gene regulation: stress-responsive microRNAs and their role in the environmental stress survival of tolerant animals

Living animals are constantly faced with various environmental stresses that challenge normal life, including: oxygen limitation, very low or high temperature, as well as restriction of water and food. It has been well established that in response to these stresses, tolerant organisms regularly respond with a distinct suite of cellular modifications that involve transcriptional, translational and post-translational modification. In recent years, a new mechanism of rapid and reversible transcriptome regulation, via the action of non-coding RNA molecules, has emerged into post-transcriptional regulation and has since been shown to be part of the survival response. However, these RNA-based mechanisms by which tolerant organisms respond to stressed conditions are not well understood. Recent studies have begun to show that non-coding RNAs control gene expression and translation of mRNA to protein, and can also have regulatory influence over major cellular processes. For example, select microRNAs have been shown to have regulatory influence over the cell cycle, apoptosis, signal transduction, muscle atrophy and fatty acid metabolism during periods of environmental stress. As we are on the verge of dissecting the roles of non-coding RNA in environmental stress adaptation, this Commentary summarizes the hallmark alterations in microRNA expression that facilitate stress survival.

Regulation of hypometabolism: insights into epigenetic controls

For many animals, survival of severe environmental stress (e.g. to extremes of heat or cold, drought, oxygen limitation, food deprivation) is aided by entry into a hypometabolic state. Strong depression of metabolic rate, often to only 1–20% of normal resting rate, is a core survival strategy of multiple forms of hypometabolism across the animal kingdom, including hibernation, anaerobiosis, aestivation and freeze tolerance. Global biochemical controls are needed to suppress and reprioritize energy use; one such well-studied control is reversible protein phosphorylation. Recently, we turned our attention to the idea that mechanisms previously associated mainly with epigenetic regulation can also contribute to reversible suppression of gene expression in hypometabolic states. Indeed, situations as diverse as mammalian hibernation and turtle anoxia tolerance show coordinated changes in histone post-translational modifications (acetylation, phosphorylation) and activities of histone deacetylases, consistent with their use as mechanisms for suppressing gene expression during hypometabolism. Other potential mechanisms of gene silencing in hypometabolic states include altered expression of miRNAs that can provide post-transcriptional suppression of mRNA translation and the formation of ribonuclear protein bodies in the nucleus and cytoplasm to allow storage of mRNA transcripts until animals rouse themselves again. Furthermore, mechanisms first identified in epigenetic regulation (e.g. protein acetylation) are now proving to apply to many central metabolic enzymes (e.g. lactate dehydrogenase), suggesting a new layer of regulatory control that can contribute to coordinating the depression of metabolic rate.

Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation

Sea cucumbers, Apostichopus japonicus, experience seasonally high water temperatures during the summer months and enter aestivation to survive. Aestivation is characterized by strong metabolic rate depression which is supported by a series of strategies including reorganizing metabolic processes, suppressing cell functions, enhancing cytoprotective mechanisms, and altered gene expression. The respiratory tree tissue of the sea cucumber is an excellent material for studying aestivation, undergoing obvious atrophy during aestivation. The present study analyzed the global gene expression profile of respiratory tree tissue of A. japonicus during aestivation by constructing and screening three libraries representing key stages of aestivation: non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA) using RNA-seq. A total of 1240, 1184 and 303 differentially expressed genes (DEGs) were identified following the criteria of |log2 ratio|≥1 and FDR≤0.001 in comparisons of DA vs. NA, AA vs. NA and DA vs. AA. A set of respiratory tree specific DEGs was identified the first time and, in addition, common DEGs that were responsive to aestivation in both respiratory tree and intestine were identified. Functional analysis of DEGs was further performed by GO enrichment analysis and respiratory tree specific GO terms were screened out and provide interesting hints for further studies of the molecular regulation of aestivation in A. japonicus.