Identification Of microRNAs Research Articles

Identification and characterization of microRNAs in Biomphalaria tenagophila and comparative analysis of their expression in Schistosoma mansoni-resistant and -susceptible snail populations

BackgroundSchistosomiasis is a neglected tropical disease caused by Schistosoma and affects over 240 million people worldwide. One of the most prominent causative agents is Schistosoma mansoni, which develops inside the intermediate host. Biomphalaria tenagophila is the second most important vector of schistosomiasis in Brazil and the Taim population is completely resistant to infection by S. mansoni. ObjectiveThis study aims to identify and characterize B. tenagophila microRNAs (miRNAs) and evaluate their differential expression in S. mansoni-susceptible and -resistant populations of B. tenagophila. MethodsTwo populations of B. tenagophila snails, susceptible and resistant to S. mansoni infection, were used to investigate the small RNA response of these snails after being infected with the parasite. Small RNA sequencing and quantitative real-time PCR were employed to identify and validate differentially expressed miRNAs. Bioinformatics analysis were performed to identify miRNA precursors and mature and evaluate their differential expression. FindingsThe study predicted 173 mature miRNAs and 123 precursors. Among them were six Lophotrochozoa-specific miRNAs, three mollusk-specific miRNAs, and six pre-miRNAs in a cluster. The small RNA sequencing and RT-PCR of B. tenagophila samples allowed assessing the expression patterns of miRNAs. Main conclusionsThe results obtained may support future studies in Biomphalaria spp., generating a global impact on disease control.

MicroRNA Identification and Integrated Network Analyses for Age-Dependent Flavonoid Biosynthesis in Ginkgo biloba

Ginkgo biloba leaves contain abundant flavonoids, and flavonoid accumulation is affected by age. MicroRNAs (miRNAs) play an important role in the plant aging pathway. However, the miRNAs involved in flavonoid biosynthesis related to age in G. biloba have rarely been studied. In this study, we compared 1-, 4-, and 7-year-old ginkgo seedings and found a significant decrease in the content of quercetin, kaempferol, and total flavonol aglycones with age. We then profiled miRNAs in G. biloba through high-throughput sequencing on leaf samples of 1-, 4-, and 7-year-old ginkgo. GO and KEGG analyses suggest that photosynthesis and hormones may influence the flavonoid content. In particular, we identified 29 miRNAs related to the aging pathway according to their miRNA expression patterns. Correlation analysis of age-related miRNAs and major flavonoid compounds screened 17 vital miRNAs, including miRN79, miR535a, miR166a, miR171a, and miR396. Interactive miRNA-transcription factor network analysis suggested that the pivotal miRN79-DELLA and miR535a-SPL modules may be involved in flavonoid biosynthesis and aging pathways through post-transcriptional regulation. Our findings provide insights into the age-dependent regulatory roles of miRNAs in flavonoid biosynthesis.

Retracted: Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics.

[This retracts the article DOI: 10.1155/2023/6457152.].

Post-Transcriptional and Epigenetic Regulation of Estrogen Signaling.

Post-translational and epigenetic regulation are important mechanisms controlling functions of genes and proteins. Although the "classic" estrogen receptors (ERs) have been acknowledged to function in mediating estrogen effects via transcriptional mechanisms, estrogenic agents modulate the turnover of several proteins via post-transcriptional and post-translational pathways including epigenetics. For instance, the metabolic and angiogenic action of G-protein coupled estrogen receptor (GPER) in vascular endothelial cells has been recently elucidated. By interacting with GPER, 17β-estradiol and the GPER agonist G1 enhance endothelial stability of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and capillary tube formation by increasing ubiquitin-specific peptidase 19 levels, thereby reducing PFKFB3 ubiquitination and proteasomal degradation. In addition to ligands, the functional expression and trafficking of ERs can be modulated by post-translational modification, including palmitoylation. MicroRNAs (miRNAs), the most abundant form of endogenous small RNAs in humans, regulate multiple target genes and are at the center of the multi-target regulatory network. This review also discusses the emerging evidence of how miRNAs affect glycolytic metabolism in cancer, as well as their regulation by estrogens. Restoring dysregulated miRNA expression represents a promising strategy to counteract the progression of cancer and other disease conditions. Accordingly, estrogen post-transcriptional regulatory and epigenetic mechanisms represent novel targets for pharmacological and nonpharmacological intervention for the treatment and prevention of hormone-sensitive noncommunicable diseases, including estrogen-sensitive cancers of the reproductive system in women. SIGNIFICANCE STATEMENT: The effects of estrogen are mediated by several mechanisms that are not limited to the transcriptional regulation of target genes. Slowing down the turnover of master regulators of metabolism by estrogens allows cells to rapidly adapt to environmental cues. Identification of estrogen-targeted microRNAs may lead to the development of novel RNA therapeutics that disrupt pathological angiogenesis in estrogen-dependent cancers.

Identification and characterization of known and new miRNAs from Nicotiana tabacum and nta-miR156's predictive role in Wnt Signalling Pathway

Computational methods have driven the rapid identification of tobacco microRNAs (miRNAs) from tissue-specific sequence data and witnessed success in associating miRNAs in response to stress, pollutants, viral infection and resistance, and cigarette smoking. Although tobacco exerted medicinal properties through phytochemicals, the role of its miRNAs in regulating tobacco and human genes and related functional implications is not elucidated thoroughly. In this present study, we have identified new and homologous miRNAs using a rigorous workflow of miRNA derivation and target prediction upon a comprehensive collection of tobacco expressed sequence tags and charted its putative roles in gene regulation via inter and intraspecies relationships. Current, computational approach have identified a total of 38 mature miRNAs comprising 31 tobacco-specific miRNAs from plant homologous families, and 7 new miRNA candidates. These seven new miRNAs were studied for tobacco target gene prediction in which most of them encode innate immunity, defense mechanism, plant development, F-box/Leucine rich-repeat protein and other protein kinases. Two out of these seven miRNAs have passed the updated emphasized criteria namely nta-miR403 and nta-miR8036. Interestingly, the workflow succeeded in establishing an intraspecies relationship by distinguishing the molecular targets already known in tobacco and homologous plants. Interspecies relationship between 38 tobacco miRNAs upon human transcriptome data revealed the most significant target CCDC88c (DAPLE) with perfect seed pairing of miR-156, regulating non-canonical WNT signaling pathways in cancer progression and metastasis. These findings may add to existing knowledge of impacting canonical WNT/β-catenin pathways. These decisive findings hold a strong clue for promoting tobacco miRNAs research and outlined the prediction of conserved miRNAs and their functions in inter and intraspecies relationships.

In silico identification and validation of microRNAs from the genome of Solanum lycopersicum targeting Groundnut bud necrosis orthotospovirus

Tomato, an extensively cultivated edible crop is prone to many viral pathogens. Among them, bud necrosis incited by Groundnut bud necrosis orthotospovirus (GBNV) causes huge yield loss (80–100%). Out of all known strategies for viral disease management in plants, RNA interference (RNAi) mediated approaches have greater potential in managing viral diseases. Small RNAs especially microRNA (miRNA) play a major role in RNAi-mediated defense in plants. Using in silico analysis, we have identified the possible tomato encoded miRNA that have the potential to interact with GBNV-mRNA. The results revealed that, sly-MIR9479-3p, sly-MIR10529, sly-MIR397-5p, sly-MIR10528, sly-MIR477-3p, and sly-MIR6024 predicted by the computational algorithms viz., miRanda, psRNA target, RNA22 and RNA hybrid have the potential to interact with different GBNV-ORFs. Conserved complementary sequences of sly-MIR10529 and sly-MIR6024, targeting GBNV genome regions (ORF2 and ORF5), were confirmed in multiple GBNV isolates. The expression of Sly-miR-10529 (1.72-fold increase),Sly-miR-6024 (2.83-fold decrease) and their corresponding glycoprotein and coat protein gene expression were quantified through q-RT-PCR. These predicted miRNAs can offer useful information for the production of antiviral agents/RNAi mediated transgenic crop plants against GBNV in tomato.

P-582 Identification of microRNA in women diagnosed with premature ovarian insufficiency using urinary exosome in Korean population

Abstract Study question Would we able to identify specific microRNA which is specific in premature ovarian insufficiency? Summary answer Our study provides compelling evidence suggesting that microRNA-4516 would be a diagnostic marker in Korean premature ovarian insufficiency women. What is known already Premature ovarian insufficiency is diagnosed in women before the age of 40 years old, when there is no menstruation for at least for six months with hypergonadotropic hypogonadism in serum evaluation. It is a disease which ovarian functions are irreversible, but women visit outpatient clinic only when their ovarian functions are already diminished. Exosomes are functional vehicles which transport complex proteins, lipids and nucleic acids between cells, containing numerous microRNAs and it may include disease-specific miRNA signature that can be a valuable diagnostic tool. Study design, size, duration This was a prospective study including patients diagnosed with premature ovarian insufficiency(POI)/Turner syndrome and control individuals who visited outpatient clinic in Department of Gynecology in Gil Hospital, Gachon University from January 2019 to August 2021. We divided the patients into two groups depending on the time period of enrollment; Sequencing cohort and Validation cohort. In sequencing cohort, total 19 patients (7/7/5) were enrolled, and in validation cohort, total 46 patients (15/11/20) were enrolled. Participants/materials, setting, methods The patients in POI group were participants diagnosed with POI but they not Turner syndrome. After collecting first morning urine samples, we extracted exosomes and RNA sequencing was done based on microRNA library. We did real-time PCR using a selected hsa-miR-4516 for confirmation. Then we did confirmation study using POI mouse model (Cyclophosphamide + Busulfan). Main results and the role of chance Expression of hsa-miR-4516 detected via qRT-PCR analysis of RNA from the validation cohort exactly mapped the RNA sequencing results of the sequencing cohort. Moreover, it was significantly upregulated in patients with POI and Turner syndrome compared to the control group. The TaqMan PCR assay confirmed the upregulation of hsa-miR-4516 expression in patients with POI and Turner syndrome. To evaluate miR-4516 as a biomarker of POI, we established a chemotherapy-induced POI mouse model by injecting the mice with CTX and BUS. Next, we assessed the expression of mmumiR-4516 in the ovaries of the chemotherapy-induced POI mouse model; mmu-miR-4516 expression was significantly increased in the ovaries but not in the uteri in the POI mouse model compared to the control. These results suggest that upregulation of mmumiR-4516 expression is associated with pathological changes in the ovaries. Limitations, reasons for caution We also observed inconsistencies between the sequencing and qRT-PCR results. The cause of POI is highly diverse, which can lead to discrepancies in exosomal miRNA expression between the cohorts. The cohort is small and limited compared to the validation cohort, and this may have caused inconsistencies between the cohorts. Wider implications of the findings We suggest that hsa-miR-4516 could be developed as a biomarker of POI within an easy and convenient diagnostic test using non-invasive sampling methods. Trial registration number -

Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain

Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain

Genome-wide identification of auxin-responsive microRNAs in the poplar stem.

Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. This report was designed to identify auxin-responsive miRNAs during wood formation. Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0mg/L, CK; 5mg/L, Low; 10mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.

Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511.

Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar Nanhui 511 (NH511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation.

Identification of key modules and micro RNAs associated with colorectal cancer via a weighted gene co-expression network analysis and competing endogenous RNA network analysis.

Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide, and the incidence of CRC has increased rapidly in recent years. Due to the high invasiveness of colonoscopy and the low accuracy of alternative diagnostic methods, the diagnosis of CRC remains a serious problem. Thus, molecular biomarkers for CRC need to be identified. In this study, RNA-sequencing data from The Cancer Genome Atlas (TCGA) database were used to identify the long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), and micro RNAs (miRNAs) that were differentially expressed between the CRC and normal tissues. Based on the gene expression and clinical features, the results of the weighted gene co-expression network analysis (WGCNA) and the binding relationships between miRNAs and lncRNAs and mRNAs were used to establish a CRC-related competing endogenous RNA (ceRNA) network. The core miRNAs (i.e., mir-874, mir-92a-1, and mir-940) in the network were identified. Among them, mir-874 was negatively correlated with the overall survival (OS) of patients. The protein-coding genes in the ceRNA network included IZUMO4, WT1, NPEPL1, TEX22, PPFIA4, and SFXN3, and the lncRNAs were LINC00858 and PRR7-AS1. These genes were significantly highly expressed in CRC according to validations in other independent data sets. In conclusion, this study established a network of the co-expressed ceRNAs associated with CRC and identified the genes and miRNAs related to the prognosis of CRC patients.

Neutrophil extracellular trap is an important connection between hemodialysis and acute myocardial infarction

The incidence of acute myocardial infarction (AMI) in hemodialysis (HD) patients is high and the prognosis is extremely poor. However, the potential connection between HD and AMI, and its regulatory mechanisms remain unclear. In this study, the gene expression profiles of HD (GSE15072) and AMI (GSE66360) were downloaded from the Gene Expression Omnibus database, common differentially expressed genes (DEGs) were obtained using the limma R package, the biological functions were analyzed according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, machine learning was conducted to identify hub genes. Receiver operating characteristic curves and gene set enrichment analyses were used to explore the characters and biological function of hub genes, networks were used for candidate identification of transcription factor (TF), microRNA (miRNA), and drug. After a total of 255 common DEGs were selected, GO and KEGG analyses indicated that neutrophil extracellular trap (NET) may be a potential connection between HD and AMI, LILRB2, S100A12, CYBB, ITGAM, and PPIF were finally identified as hub genes. The area under curve of LILRB2, S100A12, and PPIF was higher than 0.8 in both datasets. Networks show the relationship between hub genes, TF, and miRNA, also the relationship between potential drugs and protein. In conclusion, NETs may be the potential connection between AMI and HD. The potential hub gene, signaling pathways, and drugs provided by this study may contribute to future AMI prevention and intervention in HD patients.

Effect of hypoxia on the expression of microRNA in extracellular vesicles of human umbilical cord stem cells in vitro.

Mesenchymal stem cells (MSCs) derived extracellular vesicles, which have been shown to possess therapeutic effects for many diseases. However, how hypoxic conditions would affect exosomal microRNA expression in human umbilical cord MSCs (hUC-MSCs) is currently not investigated. This study aims to investigate the potential function of in vitro microRNAs of hUC-MSC cultured under normoxic and hypoxic conditions. Extracellular vesicles secreted from hUC-MSCs cultured in normoxic (21% O2) and hypoxic (5% O2) conditions were collected for microRNA identification. Zeta View Laser Scattering and transmission electron microscopy were used to observe the size and morphology of extracellular vesicles. qRT-PCR was performed to measure the expression of related microRNAs. The Gene Ontology and KEGG pathway were used to predict the function of microRNAs. Finally, the effects of hypoxia on the expression of related mRNAs and cellular activity were examined. This study identified 35 upregulated and 8 downregulated microRNAs in the hypoxia group. We performed target genes analysis to explore the potential function of these microRNA upregulated in the hypoxia group. Significant enrichment of the cell proliferation, pluripotency of stem cells, MAPK, Wnt, and adherens junction pathways were observed in the GO and KEGG pathways. Under hypoxic conditions, the expression levels of 7 target genes were lower than that of the normal environment. In conclusion, this study demonstrated for the first time that microRNA expression in extracellular vesicles of human umbilical vein stem cells cultured under hypoxia is different from that under normal conditions, and these microRNAs may be markers for detecting hypoxia.

Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.).

Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.

Identification of microRNAs implicated in modulating resveratrol-induced apoptosis in porcine granulosa cells.

MicroRNAs (miRNAs) are small, noncoding RNAs that play a crucial role in the complex and dynamic network that regulates the apoptosis of porcine ovarian granulosa cells (POGCs). Resveratrol (RSV) is a nonflavonoid polyphenol compound that is involved in follicular development and ovulation. In previous study, we established a model of RSV treatment of POGCs, confirming the regulatory effect of RSV in POGCs. To investigate the miRNA-level effects of RSV on POGCs to reveal differentially expressed miRNAs, a control group (n = 3, 0μM RSV group), a low RSV group (n = 3, 50μM RSV group), and a high RSV group (n = 3, 100μM RSV group) were created for small RNA-seq. In total, 113 differentially expressed miRNAs (DE-miRNAs) were identified, and a RT-qPCR analysis showed a correlation with the sequencing data. Functional annotation analysis revealed that DE-miRNAs in the LOW vs. CON group may be involved in cell development, proliferation, and apoptosis. In the HIGH vs. CON group, RSV functions were associated with metabolic processes and responses to stimuli, while the pathways were related to PI3K24, Akt, Wnt, and apoptosis. In addition, we constructed miRNA-mRNA networks related to Apoptosis and Metabolism. Then, ssc-miR-34a and ssc-miR-143-5p were selected as key miRNAs. In conclusion, this study provided an improved understanding of effects of RSV on POGCs apoptosis through the miRNA modulations. The results suggest that RSV may promote POGCs apoptosis by stimulating the miRNA expressions and provided a better understanding of the role of miRNAs combined with RSV in ovarian granulosa cell development in pigs.

Identification of microRNAs as diagnostic biomarkers for atrial fibrillation: a systematic review and meta-analysis.

Genetic factors contribute to the AF pathophysiology by altering the structural and functional properties of proteins involved in different cellular activities. MicroRNAs (miRNAs), which take part in structural and electrical remodeling during the AF evolution, are important genetic elements that must be considered. The aim of study is to determine correlation between the expression of miRNAs and the development of AF, as well as to explain any potential importance of genetic factors in the AF diagnosis. Online scientific databases, including Cochrane, ProQuest, PubMed, and Web of Science were used to conduct the literature search. The keywords were associated with or characterized the relationship between miRNAs and AF. The pooled sensitivity and specificity statistical parameters were analyzed using a random-effects model. The miRNAs had a combined sensitivity and specificity of 0.80 (95% CI = 0.70-0.87) and 0.75 (95% CI = 0.64-0.83) for the diagnosis of AF, respectively. The area under the SROC was 0.84 (95% CI = 0.81-0.87). The DOR was 11.80 (95% CI = 6.79-20.50). This study also revealed that miRNAs had a pooled PLR of 3.16 (95% CI = 2.24-4.45) and NLR of 0.27 (95% CI = 0.18-0.39) for the diagnosis of AF. The miR-425-5p demonstrated the highest sensitivity (0.96, 95% CI, 0.89-0.99). The meta-analysis revealed substantial connection between miRNA expression dysregulation and AF, supporting the potential diagnostic role of miRNAs. The miR-425-5p has potential role as a biomarker for AF.

Identification of novel microRNAs in the embryonic mouse brain using deep sequencing

Many advances in small RNA-seq technology and bioinformatics pipelines have been made recently, permitting the discovery of novel miRNAs in the embryonic day 15.5 (E15.5) mouse brain. We aimed to improve miRNA discovery in this tissue to expand our knowledge of the regulatory networks that underpin normal neurodevelopment, find new candidates for neurodevelopmental disorder aetiology, and deepen our understanding of non-coding RNA evolution. A high-quality small RNA-seq dataset of 458 M reads was generated. An unbiased miRNA discovery pipeline identified fifty putative novel miRNAs, six of which were selected for further validation. A combination of conservation analysis and target functional prediction was used to determine the authenticity of novel miRNA candidates. These findings demonstrate that miRNAs remain to be discovered, particularly if they have the features of other small RNA species.

Identification of MicroRNAs Regulating Clostridium perfringens Type C Infection in the Spleen of Diarrheic Piglets

Clostridium perfringens (C. perfringens) type C is one of the common bacteria in piglet diarrhea, which seriously affects the swine industry's development. The spleen plays crucial roles in the resistance and elimination of pathogenic microorganisms, and miRNAs play important roles in regulating piglet diarrhea caused by pathogens. However, the mechanism by which miRNAs in the spleen are involved in regulating C. perfringens type C causing diarrhea in piglets remains unclear. The expression profiles of the spleen miRNAs of 7-day-old piglets challenged by C. perfringens type C were studied using small RNA-sequencing in control (SC), susceptible (SS), and resistant (SR) groups. Eight-eight differentially expressed miRNAs were screened. The KEGG pathway analysis of target genes revealed that the miRNAs were involved in the MAPK, p53, and ECM-receptor interaction signaling pathways. NFATC4 was determined to be a direct target of miR-532-3p and miR-133b using a dual-luciferase reporter assay. Thus, miR-133b and miR-532-3p targeted to NFATC4 were likely involved to piglet resistance to C. perfringens type C. This paper provides the valuable resources to deeply understand the genetic basis of C. perfringens type C resistance in piglets and a solid foundation to identify novel markers of C. perfringens type C resistance.

Identification and Characterization of Development-Related microRNAs in the Red Flour Beetle, Tribolium castaneum

MicroRNAs (miRNAs) play important roles in insect growth and development, but they were poorly studied in insects. In this study, a total of 883 miRNAs were detected from the early embryo (EE), late larva (LL), early pupa (EP), late pupa (LP), and early adult (EA) of Tribolium castaneum by microarray assay. Further analysis identified 179 differentially expressed unique miRNAs (DEmiRNAs) during these developmental stages. Of the DEmiRNAs, 102 DEmiRNAs exhibited stage-specific expression patterns during development, including 53 specifically highly expressed miRNAs and 20 lowly expressed miRNAs in EE, 19 highly expressed miRNAs in LL, 5 weakly expressed miRNAs in EP, and 5 abundantly expressed miRNAs in EA. These miRNAs were predicted to target 747, 265, 472, 234, and 121 genes, respectively. GO enrichment analysis indicates that the targets were enriched by protein phosphorylation, calcium ion binding, sequence-specific DNA binding transcription factor activity, and cytoplasm. An RNA interference-mediated knockdown of the DEmiRNAs tca-miR-6-3p, tca-miR-9a-3p, tca-miR-9d-3p, tca-miR-11-3p, and tca-miR-13a-3p led to defects in metamorphosis and wing development of T. castaneum. This study has completed the identification and characterization of development-related miRNAs in T. castaneum, and will enable us to investigate their roles in the growth and development of insect.

Identification and characterization of microRNAs, especially gga-miR-181b-5p, in chicken macrophages associated with avian pathogenic E. coli infection

ABSTRACT Avian pathogenic E. coli (APEC) is a common pathogen in the poultry industry, which can cause substantial economic losses. Recently, emerging evidence showed that miRNAs were involved in various viral and bacterial infections. To elucidate the role of miRNAs in chicken macrophages in response to APEC infection, we attempted to investigate the miRNAs expression pattern upon APEC infection via miRNA-seq, and to identify the molecular mechanism of the important miRNAs by using RT-qPCR, western blotting, dual-luciferase reporter assay, and CCK-8. The results showed that a total of 80 differentially expressed (DE) miRNAs were identified in comparison of APEC vs. wild-type group, which corresponded to 724 target genes. Moreover, the target genes of the identified DE miRNAs were mainly significantly enriched in the MAPK signalling pathway, autophagy-bird, mTOR signalling pathway, ErbB signalling pathway, Wnt signalling pathway, and TGF-beta signalling pathway. Remarkably, gga-miR-181b-5p is able to participate in host immune and inflammatory responses against APEC infection via targeting of TGFBR1 to modulate the activation of TGF-beta signalling pathway. Collectively, this study provides a perspective of miRNA expression patterns in chicken macrophages upon APEC infection. These findings provide insight into miRNAs against APEC infection, and gga-miR-181b-5p might be a potential target for treating APEC infection.