Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals

Analysis of Amblyomma americanum microRNAs in response to Ehrlichia chaffeensis infection and their potential role in vectorial capacity

Background

MicroRNAs (miRNAs) represent a subset of small noncoding RNAs and carry tremendous potential for regulating gene expression at the post-transcriptional level. They play pivotal roles in distinct cellular mechanisms including inhibition of bacterial, parasitic, and viral infections via immune response pathways. Intriguingly, pathogens have developed strategies to manipulate the host's miRNA profile, fostering environments conducive to successful infection. Therefore, changes in an arthropod host's miRNA profile in response to pathogen invasion could be critical in understanding host-pathogen dynamics. Additionally, this area of study could provide insights into discovering new targets for disease control and prevention. The main objective of the present study is to investigate the functional role of differentially expressed miRNAs upon Ehrlichia chaffeensis, a tick-borne pathogen, infection in tick vector, Amblyomma americanum.

Methods

Small RNA libraries from uninfected and E. chaffeensis-infected Am. americanum midgut and salivary gland tissues were prepared using the Illumina Truseq kit. Small RNA sequencing data was analyzed using miRDeep2 and sRNAtoolbox to identify novel and known miRNAs. The differentially expressed miRNAs were validated using a quantitative PCR assay. Furthermore, a miRNA inhibitor approach was used to determine the functional role of selected miRNA candidates.

Results

The sequencing of small RNA libraries generated >147 million raw reads in all four libraries and identified a total of >250 miRNAs across the four libraries. We identified 23 and 14 differentially expressed miRNAs in salivary glands, and midgut tissues infected with E. chaffeensis, respectively. Three differentially expressed miRNAs (miR-87, miR-750, and miR-275) were further characterized to determine their roles in pathogen infection. Inhibition of target miRNAs significantly decreased the E. chaffeensis load in tick tissues, which warrants more in-depth mechanistic studies.

Conclusions

The current study identified known and novel miRNAs and suggests that interfering with these miRNAs may impact the vectorial capacity of ticks to harbor Ehrlichia. This study identified several new miRNAs for future analysis of their functions in tick biology and tick-pathogen interaction studies.

Analysis of Amblyomma americanum microRNAs in response to Ehrlichia chaffeensis infection and their potential role in vectorial capacity

Background

MicroRNAs (miRNAs) represent a subset of small noncoding RNAs and carry tremendous potential for regulating gene expression at the post-transcriptional level. They play pivotal roles in distinct cellular mechanisms including inhibition of bacterial, parasitic, and viral infections via immune response pathways. Intriguingly, pathogens have developed strategies to manipulate the host's miRNA profile, fostering environments conducive to successful infection. Therefore, changes in an arthropod host's miRNA profile in response to pathogen invasion could be critical in understanding host-pathogen dynamics. Additionally, this area of study could provide insights into discovering new targets for disease control and prevention. The main objective of the present study is to investigate the functional role of differentially expressed miRNAs upon Ehrlichia chaffeensis, a tick-borne pathogen, infection in tick vector, Amblyomma americanum.

Methods

Small RNA libraries from uninfected and E. chaffeensis-infected Am. americanum midgut and salivary gland tissues were prepared using the Illumina Truseq kit. Small RNA sequencing data was analyzed using miRDeep2 and sRNAtoolbox to identify novel and known miRNAs. The differentially expressed miRNAs were validated using a quantitative PCR assay. Furthermore, a miRNA inhibitor approach was used to determine the functional role of selected miRNA candidates.

Results

The sequencing of small RNA libraries generated >147 million raw reads in all four libraries and identified a total of >250 miRNAs across the four libraries. We identified 23 and 14 differentially expressed miRNAs in salivary glands, and midgut tissues infected with E. chaffeensis, respectively. Three differentially expressed miRNAs (miR-87, miR-750, and miR-275) were further characterized to determine their roles in pathogen infection. Inhibition of target miRNAs significantly decreased the E. chaffeensis load in tick tissues, which warrants more in-depth mechanistic studies.

Conclusions

The current study identified known and novel miRNAs and suggests that interfering with these miRNAs may impact the vectorial capacity of ticks to harbor Ehrlichia. This study identified several new miRNAs for future analysis of their functions in tick biology and tick-pathogen interaction studies.

Integrated analysis of expression profiles with meat quality traits in cattle

MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.

Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii)

Background

The formation of musk is a complex biophysical and biochemical process that change with the rut of male forest musk deer. We have reported that the mating status of male forest musk deer might result to the variations of chemical composition and microbiota of musk and its yields. Critical roles for microRNAs (miRNAs) of multi-tissues were profiled in our previous study; however, the role for miRNAs of the musk gland remains unclear in this species.

Methods

In this study, we used Illumina deep sequencing technology to sequence the small RNA transcriptome of unmated male (UM) and mated male (UM) of Chinese forest musk deer.

Results

We identified 1,652 known miRNAs and 45 novel miRNAs, of which there were 174 differentially expressed miRNAs between UM and MM. chi-miR-21-5p, ipu-miR-99b and bta-miR-26a were up-regulated in UM among the 10 most differentially expressed miRNAs. Functional enrichment of the target genes showed that monosaccharide biosynthetic process, protein targeting, cellular protein catabolic process enriched higher in MM. Meanwhile, structural molecule activity, secretion by cell, regulated exocytosis and circulatory system process enriched more in UM, hinting that the formation of musk in UM was mediated by target genes related to exocytosis. The miRNA-mRNA pairs such as miR-21: CHD7, miR143: HSD17B7, miR-141/200a: Noc2 might involve in musk gland development and musk secretion, which need to be verified in future study.

miR300 intervenes Smad3/β-catenin/RunX2 crosstalk for therapy with an alternate function as indicative biomarker in osteoporosis

The study reports a theranostic nature of rno-miR-300 (miR300) in the osteoblast functioning, by influencing the signaling pathway(s), associated with osteoblast differentiation. Excessive expression of miR300 suppresses osteoblast functions. Smad3 served as a validated target for miR300, on homology-based computational analysis and experimental testimony, which activates β-catenin, and subsequently potentiates Runx2. The impact of miR300 on the Smad3/β-catenin/Runx2 signaling interactions in the induction of osteoblast differentiation was scrutinized by immunoblotting and in vivo miRNA antagonism. Overexpression of miR300 in the rat calvarial osteoblasts decreases the protein levels of Smad3, β-catenin and Runx2. Besides, in vivo silencing of miR300 in the neonatal pups and adult rats by AntimiR300 abolishes the suppressing action of miR300 on the osteoblast differentiation and expressions of Smad3/β-catenin/Runx2 axis. MicroCT studies showed improved trabecular microarchitecture in the AntimiR300 transfected ovariectomised rat model compared to sham and negative control. Furthermore, expression levels of miR300 were evaluated in serum samples from an independent set of 30 osteoporotic patients followed by a Receiver Operating Characteristic Curve (ROC) based analysis for the diagnostic efficiency of miR300. Interestingly, the results exhibited high levels of miR300 (p < 0.0001) in the serum samples from osteoporotic patients relative to non-osteoporotic subjects (AUC = 0.9689). Thus, miR300 negatively regulates the differentiation of osteoblasts by targeting crosstalk among Smad3, β-catenin and Runx2, unveiling an enormous ability to serve as a therapeutic target for bone-related disorder management strategies. Besides, miR300 may potentially function for the diagnosis of osteoporosis as a non-invasive biomarker.

In-silico investigations of selective miRNA-gene targets and their validation studies in obstructive sleep apnea (OSA) patient cohorts

BACKGROUND

Obstructive sleep apnoea (OSA) is a prevalent form of sleep disordered breathing which results in sleep fragmentation and deprivation. Obesity and cardiovascular disorders are the major risk factors associated with OSA. Molecular analysis of the factors associated with OSA could demarcate the clinical analysis pattern in a population.

OBJECTIVE

This study pertains to in-silico analyses of miRNA and their gene targets with validation for their potential role in OSA as putative biomarker candidates.

METHODS

miRDB, TargetScan and miRanda databases were used to identify targets of miR-27 and let-7 that have documented role in OSA and co-related obesity and cardiovascular disorders. Quantitative PCR was used to analyze expression pattern of miR-27 and let-7 in obese and non-obese OSA patient cohorts with respective controls. In-silico analysis was done using PatchDoc to obtain atomic contact energy (ACE) scores that indicated the docked gene targets to the predicted miRNA structures. The docked structures were analysed using Maestro Suite 11 for the hydrogen and aromatic interactions.

RESULTS

Downregulation of miR-27 and let-7 in OSA compared to controls was observed. In-silico data analysis was performed for gene targets (TGFBR1, TGFBR2, SMAD2, SMAD4, CRY2 and CNR1) of the selected miRNAs (miR-27 and let-7). Among all, CNR1 and CRY2 were found to be better targets for miR-27 and let-7 respectively as per ACE scores, ROC scores and expression fold change in OSA.

CONCLUSION

Our study gives insights to the expression profiling of miR-27 and let-7 and explore a set of potential target genes (CNR1 and CRY2) of these two miRNAs for a promising clinical relevance in OSA.

Screening of miRNA target genes in coronary artery disease by variational Bayesian Gaussian mixture model

Coronary artery disease (CAD) is a leading cause of death, and microRNAs (miRNAs) are widely involved in physiological and pathological processes of CAD. We chose the targetscore method calculated via the variational Bayesian Gaussian mixture model (VB-GMM) as the prediction method of target genes. By observing the density overlap, we selected the thresholds of miRNA-1 and miRNA-155. In total, 18 target genes of miRNA-1, and 19 target genes of miRNA-155 were identified. The threshold of miRNA-146a was selected using the |logFC| value, and 16 target genes were screened out. In this study, our major contribution was to predict the target messenger RNAs (mRNAs) of the chosen miRNAs with the gene expression profiles, which can effectively reduce the workload of screening. Although the validated genes constituted only a small part in the final prediction results, it is a good sign for research in the future. It means that we could provide new research aims for future studies focusing on miRNA regulatory mechanisms.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.

Is the Efficiency of RNA Silencing Evolutionarily Regulated?

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) regulate gene expression in a sequence-specific manner. Genes with partial complementarity to siRNA/miRNA sequences in their 3′-untranslated regions (UTRs) are suppressed by a mechanism referred to as the siRNA off-target effect or miRNA-mediated RNA silencing. However, the determinants of such RNA silencing efficiency are poorly understood. Previously, I and co-workers reported that the efficiency of RNA silencing is strongly correlated with the thermodynamic stability of base pairing in the duplex formed within an siRNA/miRNA and between the seed region and its target mRNA. In this review, I first summarize our previous studies that identified the thermodynamic parameter to estimate the silencing efficiency using the calculated base pairing stability: siRNAs downregulate the expression of off-target genes depending on the stability of binding between the siRNA seed region (nucleotides 2–8) and off-target mRNAs, and miRNAs downregulate target mRNA expression depending on the stability of the duplex formed between the 5′ terminus of the miRNA and its target mRNA. I further discuss the possibility that such thermodynamic features of silencing efficiency may have arisen during evolution with increasing body temperature in various organisms.

Genome-wide identification and characterization of microRNA genes and their targets in large yellow croaker (Larimichthys crocea)

MicroRNAs (miRNAs or miRs) are a class of non-coding RNAs of 20-25 nucleotides (nt) in length, which regulates the expression of gene in eukaryotic organism. Studies has been confirmed that miRNA plays an important role in various biological and metabolic processes in both animals and plants. Predicting new miRNAs by computer based homology search analysis is an effective way to discover novel miRNAs. Though a large number of miRNAs have been reported in many fish species, reports of miRNAs in large yellow croaker (L. crocea) are limited especially via the computational-based approaches. In this paper, a method of comparative genomic approach by computational genomic homology based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. A total of 199 potential miRNAs were predicted representing 81 families. 12 of them were chose to be validated by real time RT-PCR, apart from miR-7132b-5p which was not detected. Results indicated that the prediction method that we used to identify the miRNAs was effective. Furthermore, 948 potential target genes were predicted. Gene ontology (GO) analysis revealed that 175, 287, and 486 target genes were involved in cellular components, biological processes and molecular functions, respectively. Overall, our findings provide a first computational identification and characterization of L. crocea miRNAs and their potential targets in functional analysis, and will be useful in laying the foundation for further characterization of their role in the regulation of diversity of physiological processes.

Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp)

MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a "living fossil," whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed its miRNAs and the components of its RNAi machinery. We used deep sequencing to analyze small RNA libraries from the six different developmental stages of T. cancriformis (egg, first-fourth instars, and adult), and also analyzed its genomic DNA with deep sequencing. We identified 180 miRNAs (87 conserved miRNAs and 93 novel candidate miRNAs), and deduced the components of its RNAi machinery: the DICER1, AGO1-3, PIWI, and AUB proteins. A comparative miRNA analysis of T. cancriformis and Drosophila melanogaster showed inconsistencies in the expression patterns of four conserved miRNAs. This suggests that although the miRNA sequences of the two species are very similar, their roles differ across the species. An miRNA conservation analysis revealed that most of the conserved T. cancriformis miRNAs share sequence similarities with those of arthropods, although T. cancriformis is called a "living fossil." However, we found that let-7 and DICER1 of T. cancriformis are more similar to those of the vertebrates than to those of the arthropods. These results suggest that miRNA systems of T. cancriformis have evolved in a unique fashion.

Prediction and characterization of microRNAs from eleven fish species by computational methods

MicroRNAs (miRNAs) are a family of single-stranded RNA molecules about 22 nt in length, which can regulate protein-coding gene expression in various organisms by post-transcriptional repression of messenger. In this research, the potential miRNAs and their target genes were analyzed and predicted by computational methods from the EST and GSS databases of eleven fish species, 43 potential miRNAs were identified, they belong to 38 miRNA families, some miRNAs are highly conserved in animal kingdom, the predicted target genes are involved in development, signal transduction, response to environmental stress and pathogen invasion. Taken together, our data suggest that there are a plentiful of miRNAs in these eleven fish species, these miRNAs may play some important roles by regulating their target genes, and the data provide important information for further functional studies.

Autophagy and microRNA dysregulation in liver diseases

Autophagy is a catabolic process through which organelles and cellular components are sequestered into autophagosomes and degraded via fusion with lysosomes. Autophagy plays a role in many physiological processes, including stress responses, energy homeostasis, elimination of cellular organelles, and tissue remodeling. In addition, autophagy capacity changes in various disease states. A series of studies have shown that autophagy is strictly controlled to maintain homeostatic balance of energy metabolism and cellular organelle and protein turnover. These studies have also shown that this process is post-transcriptionally controlled by small noncoding microRNAs that regulate gene expression through complementary base pairing with mRNAs. Conversely, autophagy regulates the expression of microRNAs. Therefore, dysregulation of the link between autophagy and microRNA expression exacerbates the pathogenesis of various diseases. In this review, we summarize the roles of autophagy and microRNA dysregulation in the course of liver diseases, with the aim of understanding how microRNAs modify key autophagic effector molecules, and we discuss how this dysregulation affects both physiological and pathological conditions. This article may advance our understanding of the cellular and molecular bases of liver disease progression and promote the development of strategies for pharmacological intervention.

Computational Identification of MicroRNAs from the Expressed Sequence Tags of Toxic Dinoflagellate Alexandrium Tamarense

Micro ribonucleic acids (miRNAs) represent a class of small noncoding RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or by repressing mRNA translation. In the case of algal lineages, especially dinoflagellates, knowledge regarding the miRNA system is still limited and its regulatory role remains unclear. In the present study, a computational approach was employed to screen miRNAs from the expressed sequence tags (ESTs) of Alexandrium tamarense. A total of 18 potential miRNAs were identified according to a range of filtering criteria. In addition, unique evolutionary features, such as miRNA gene duplication and sequence similarity to metazoan miRNAs, implied that the miRNA system in dinoflagellates is complex. Moreover, based on these 18 miRNA sequences, 42 potential target genes showing diverse functions in regulating growth and development were predicted in Thalassiosira pseudonana and Phaeodactylum tricornutum. Taken together, our data suggest the existence of miRNAs in dinoflagellates and provide clues for further functional studies on these predicted miRNAs.

Stability of miRNA 5'terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy

MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly understood. Here we mathematized base-pairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity. The results are consistent with the previous findings that an RNA strand with unstable 5′ terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and miRNA recognizes target mRNAs with seed-complementary sequences to direct posttranscriptional repression. Our results suggested that both the unwinding and target recognition processes of miRNAs could be proficiently controlled by the thermodynamics of base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might be evolutionarily well adapted to the body temperatures of various species.

Human hepatocellular carcinoma cell-specific miRNAs reveal the differential expression of miR-24 and miR-27a in cirrhotic/non-cirrhotic HCC

microRNAs (miRs) are 18–25 nucleotide non-coding RNAs that regulate gene expression in several physiological and pathological conditions. To gather more knowledge on microRNAs in human hepatocellular carcinoma (HCC) we generated a small RNA library in the human HCC cell line HA22T/VGH by cloning and sequencing the cDNA obtained following the size selection of 18–24 nucleotide RNAs. We determined the expression levels of the most frequently cloned microRNAs by qPCR in HCC tissues and in their peritumoral counterparts from biopsy specimens of 41 HCC patients. The most frequently cloned miRs were miR-24, miR-27a and miR-21, and their expression levels in human HCC tissues indicate that these miRs were dysregulated in HCC. We showed that miR-24 and miR-27a were significantly downregulated in HCCs from cirrhotic liver tissues in comparison to those from non-cirrhotic liver tissues. In cirrhotic HCCs the downregulation of miR-24 was correlated with poorer prognosis in patients with HBV and HCV virus infections. miR-21 was generally upregulated in HCC tissues versus the corresponding peritu-moral tissues, particularly in non-cirrhotic HCC. Furthermore, by sequence alignment we identified the human miR orthologue of Mus musculus miR-1199 not yet annotated. Our results outline the differential expression of miRs in cirrhotic and non-cirrhotic HCCs, thereby contributing to advances in the discovery and validation of novel molecular biomarkers of HCC progression.

An antagomir to microRNA Let7f promotes neuroprotection in an ischemic stroke model

We previously showed that middle-aged female rats sustain a larger infarct following experimental stroke as compared to younger female rats, and paradoxically, estrogen treatment to the older group is neurotoxic. Plasma and brain insulin-like growth factor-1 (IGF-1) levels decrease with age. However, IGF-1 infusion following stroke, prevents estrogen neurotoxicity in middle-aged female rats. IGF1 is neuroprotective and well tolerated, but also has potentially undesirable side effects. We hypothesized that microRNAs (miRNAs) that target the IGF-1 signaling family for translation repression could be alternatively suppressed to promote IGF-1-like neuroprotection. Here, we report that two conserved IGF pathway regulatory microRNAs, Let7f and miR1, can be inhibited to mimic and even extend the neuroprotection afforded by IGF-1. Anti-mir1 treatment, as late as 4 hours following ischemia, significantly reduced cortical infarct volume in adult female rats, while anti-Let7 robustly reduced both cortical and striatal infarcts, and preserved sensorimotor function and interhemispheric neural integration. No neuroprotection was observed in animals treated with a brain specific miRNA unrelated to IGF-1 (anti-miR124). Remarkably, anti-Let7f was only effective in intact females but not males or ovariectomized females indicating that the gonadal steroid environment critically modifies miRNA action. Let7f is preferentially expressed in microglia in the ischemic hemisphere and confirmed in ex vivo cultures of microglia obtained from the cortex. While IGF-1 was undetectable in microglia harvested from the non-ischemic hemisphere, IGF-1 was expressed by microglia obtained from the ischemic cortex and was further elevated by anti-Let7f treatment. Collectively these data support a novel miRNA-based therapeutic strategy for neuroprotection following stroke.

MicroRNAs: potentially important regulators for schistosome development and therapeutic targets against schistosomiasis

MicroRNAs (miRNAs) are small, endogenous non-coding RNA molecules that regulate gene expression post-transcriptionally by targeting the 3' untranslated region (3' UTR) of messenger RNAs. Since the discovery of the first miRNA in Caenorhabditis elegans, important regulatory roles for miRNAs in many key biological processes including development, cell proliferation, cell differentiation and apoptosis of many organisms have been described. Hundreds of miRNAs have been identified in various multicellular organisms and many are evolutionarily conserved. Schistosomes are multi-cellular eukaryotes with a complex life-cycle that require genes to be expressed and regulated precisely. Recently, miRNAs have been identified in two major schistosome species, Schistosoma japonicum and S. mansoni. These miRNAs are likely to play critical roles in schistosome development and gene regulation. Here, we review recent studies on schistosome miRNAs and discuss the potential roles of miRNAs in schistosome development and gene regulation. We also summarize the current status for targeting miRNAs and the potential of this approach for therapy against schistosomiasis.

miR-124, miR-125b, let-7 and vesicle transport proteins in squid lenses in L. pealei

PURPOSE

Studies over the past several decades identified parallels between neuron and lens fiber cell morphology, development, and physiology. Consistent with this, mammalian lens fiber cells were shown to express a substantial complement of genes that cluster with respect to synaptic vesicle transport and exocytosis. Expression of these genes in these two cell types also appears consistent with similarities described between lens fiber cell lateral protrusions and neuronal dendrites. Recently, we showed vertebrate neurons and lens fiber cells share expression of a core set of factors that form an interlocking regulatory network which has a fundamental role in determining neural cell identity. These included the REST/NRSF transcription factor, neural RNA binding proteins and miR-124. In addition, we identified miR-125 and let-7 in mammalian lenses that have been shown to regulate dendrite formation in neurons. The present study examined expression of miR-124, miR-125, and let-7 as well as genes involved in vesicle transport in lens in the squid Loligo (also referred to as Doryteuthis) pealei.

METHODS

Northern blot, RT-PCR, immunoblots, and in situ detection were used to analyze expression in squid and vertebrate tissues.

RESULTS

The present study provided evidence that miR-124, miR-125, let-7 and vesicle transport-related proteins are produced in squid lenses. Consistent with these mRNAs and miRNAs in squid lenses, and polyribosomes shown by others, we detected substantial levels of tRNA and rRNA in anuclear squid lenses which do not produce an epithelial cell layer that would be analogous to vertebrate lenses.

CONCLUSIONS

Our study provided evidence that miR-124, miR-125, and let-7, as well as proteins involved in vesicle transport linked with synaptic and cargo vesicle transport in vertebrates are also expressed in squid lenses.

miRNA-mediated immune regulation and immunotherapeutic potential in glioblastoma

Glioblastoma (GB), the most common primary neoplasm of the CNS, remains universally fatal with standard therapies and has a mean overall survival time of only 14.6 months. Even in the most favorable situations most patients do not survive longer than 2 years. Another hallmark of GBs, apart from the poor control of proliferation, is an immune suppressed tumor microenvironment. miRNAs usually bind the 3' untranslated region of target mRNAs and direct their post-transcriptional repression. Certain miRNAs are known to have altered expression levels in GB tumors, and in many immune cell subtypes. miRNAs have been found to serve important roles in gene regulation and are implicated in many processes in oncogenesis and immune deregulation. In this article we focus on the miRNAs involved in gliomagenesis and in the regulation of the immune response. We also present current challenges and miRNA immunotherapeutic strategies that should be investigated further.

Evaluation of online miRNA resources for biomedical applications

MicroRNAs (miRNAs) are endogenous single-stranded, 22-nt (nucleotide) RNAs which complement mRNA to initiate post-transcriptional regulation. This review presents updates and evaluations of the public domain resources available for miRNA identification and target prediction toward their utilization in the biomedical research approach. This study discusses the basic principles of miRNA computational studies based on the nature and mechanism of action of miRNAs. Furthermore, we have explored fifty-nine current online miRNA tools that can be categorized into three classes in this paper: (i) miRNA identification; (ii) miRNA target prediction; and (iii) specialized miRNA tools.

Systems Biology Reveals MicroRNA-Mediated Gene Regulation

MicroRNAs (miRNAs) are members of the small non-coding RNAs, which are principally known for their functions as post-transcriptional regulators of target genes. Regulation by miRNAs is triggered by the translational repression or degradation of their complementary target messenger RNAs (mRNAs). The growing number of reported miRNAs and the estimate that hundreds or thousands of genes are regulated by them suggest a magnificent gene regulatory network in which these molecules are embedded. Indeed, recent reports have suggested critical roles for miRNAs in various biological functions, such as cell differentiation, development, oncogenesis, and the immune responses, which are mediated by systems-wide changes in gene expression profiles. Therefore, it is essential to analyze this complex regulatory network at the transcriptome and proteome levels, which should be possible with approaches that include both high-throughput experiments and computational methodologies. Here, we introduce several systems-level approaches that have been applied to miRNA research, and discuss their potential to reveal miRNA-guided gene regulatory systems and their impacts on biological functions.

Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni

Mature microRNAs (miRNAs) are small, non-coding regulatory RNAs which can elicit post-transcriptional repression of mRNA levels of target genes. Here, we report the identification of 67 mature and 42 precursor miRNAs in the Schistosoma mansoni parasite. The evolutionarily conserved S. mansoni miRNAs consisted of 26 precursor miRNAs and 35 mature miRNAs, while we identified 16 precursor miRNAs and 32 mature miRNAs that displayed no conservation. These S. mansoni miRNAs are located on seven autosomal chromosomes and a sex (W) chromosome. miRNA expansion through gene duplication was suggested for at least two miRNA families miR-71 and mir-2. miRNA target finding analysis identified 389 predicted mRNA targets for the identified miRNAs and suggests that the sma-mir-71 may be involved in female sexual maturation. Given the important roles of miRNAs in animals, the identification and characterization of miRNAs in S. mansoni will facilitate novel approaches towards prevention and treatment of Schistosomiasis.