miRNA target recognition identification

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus . Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies...

Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is the causative virus of the pandemic coronavirus disease 2019 (COVID-19). Evaluating the immunological factors and other implicated processes underlying the progression of COVID-19 is essential for the recognition and then the design of efficacious therapies. Therefore, we analyzed RNAseq data obtained from PBMCs of the COVID-19 patients to explore coding and non-coding RNA diagnostic immunological panels. For this purpose, we integrated multiple RNAseq data and analyzed them overall as well as by considering the state of disease including severe and non-severe conditions...

Accurate and sensitive analysis of biomarkers is a promising way to provide comprehensive physio-pathological information that is significant for early diagnosis of certain diseases. miRNA is a type of noncoding small RNAs which are involved in the regulation of a number of cellular processes. It has been regarded as an important tumor biomarker. Herein, we have constructed a three-dimensional DNA layer on electrode interface and achieved ladder hybridization chain reaction strategy for the enrichment of electrochemical signals...

The identification of tumor-related microRNAs (miRNAs) exhibits excellent promise for the early diagnosis of cancer and other bioanalytical applications. Therefore, we developed a sensitive and efficient biosensor using polyadenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) for miRNA analysis based on strand displacement reactions on gold nanoparticle (AuNP) surfaces and electrokinetic signal amplification (ESA) on a microfluidic chip. In this FSNA, polyA-DNA biosensor was anchored on AuNP surfaces via intrinsic affinity between adenine and Au...

Circular RNAs (circRNAs) are known to act as important regulators of the microRNA (miRNA) activity. Yet, computational resources to identify miRNA:circRNA interactions are mostly limited to already annotated circRNAs or affected by high rates of false positive predictions. To overcome these limitations, we developed Circr, a computational tool for the prediction of associations between circRNAs and miRNAs. Circr combines three publicly available algorithms for de novo prediction of miRNA binding sites on target sequences (miRanda, RNAhybrid, and TargetScan) and annotates each identified miRNA:target pairs with experimentally validated miRNA:RNA interactions and binding sites for Argonaute proteins derived from either ChIPseq or CLIPseq data...

Chronic neuropathic pain is commonly accompanied by cognitive impairment. However, the underlying mechanism in the occurrence of cognitive deficits under constant nociceptive irritation remains elusive. Herein, we established a chronic neuropathic pain model by chronic constriction injury (CCI) of the unilateral sciatic nerve in rats. Behavioral tests indicated that CCI rats with long-term nociceptive threshold decline developed significant dysfunction of working memory and recognitive memory starting at 14 days and lasting for at least 21 days...

Rapid and sensitive detection of biomarkers enables monitoring patients' health status and can enhance the early diagnosis of deadly diseases. In this work, we have developed a new colorimetric platform based on spherical nucleic acid (SNA) and G-quadruplex DNAzymes for the identification of specific miRNAs. The simple hybridization between the target miRNA and two capture probes (capture probe 1 located at AuNP surface and free capture probe 2) is the working principle of this biosensor. The hybridization and duplex formation among probes and miRNAs led to a significant decrease in the intensity of color change...

BACKGROUND: Immune checkpoint inhibitors directed against programmed cell death 1 (PDCD1/PD1) receptor and programmed cell death-ligand 1 (CD274/PD-L1) have been recently successfully implemented for the treatment of many cancers, but the response rate of tumour patients is still limited due to intrinsic and acquired resistances. However, the underlying molecular mechanisms of this limited response have still to be defined in detail. The aim of this study is to uncover processes inhibiting PDCD1/CD274 expression thereby enhancing anti-tumour immune responses...

Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact, and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small RNAs (sRNAs) are vital components of posttranscriptional gene regulation, although their role in gene expression regulation during mycoparasitisms remain understudied...

Background: Chronic neuropathic pain is commonly associated with memory loss, which increases the risk of dementia, lowers life quality and spending. On the other hand, the molecular processes are unknown, and effective therapies have yet to be discovered. Long non-coding RNAs (lncRNAs) are emerging potential therapeutic targets for chronic pain, but their role in chronic pain-induced memory impairment is unknown. Methods: We established a CCI-induced memory impairment rat model. To investigate and validate the gene expression alterations in the hippocampus of CCI-induced memory impairment, we used RNA-Seq, bioinformatics analysis, qRT-PCR, western blot, immunostaining, Nissl staining, and Diaminobenzidine-enhanced Perls' stain...

Coronaviruses are a family of viruses that infect mammals and birds. Coronaviruses cause infections of the respiratory system in humans, which can be minor or fatal. A comparative transcriptomic analysis has been performed to establish essential profiles of the gene expression of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) linked to cystic fibrosis (CF). Transcriptomic studies have been carried out in relation to SARS-CoV-2 since a number of people have been diagnosed with CF. The recognition of differentially expressed genes demonstrated 8 concordant genes shared between the SARS-CoV-2 and CF...

BACKGROUND: In the last decade among the current cancers, skin cancer is emerging and rising rapidly. The melanoma and non-melanoma type contributed mainly to skin cancer and is considered metastatic and deadly. Extreme exposure to ultra-violet radiation (depletion of the ozone layer or industry exposure) leads to an enormous rise in cases of skin cancers. OBJECTIVES: The previous therapy includes surgery, chemotherapy, and radiation which are invasive methods and greatly associated with several adverse effects on healthy tissues...

Retinoblastoma (Rb) is the most common childhood malignancy initiated by biallelic mutation in RB1 gene and driven by various epigenetic events including DNA methylation and microRNA dysregulation. Hence, understanding the key genes that are critically modulated by epigenetic modifications in RB1 -/- cells is very important to identify prominent biomarkers and therapeutic targets of Rb. In this study, we for the first time have integrated various Rb microarray NCBI-GEO datasets including DNA Methylation (GSE57362), miRNA (GSE7072) and mRNA (GSE110811) to comprehensively investigate the epigenetic consequences of RB loss in retinoblastoma tumors and identify genes with the potential to serve as early diagnostic markers and therapeutic targets for Rb...

BACKGROUND: Multiple myeloma (MM) is a complex disease affected by many factors. The recognition of miRNA networks is helpful for specific detection and personalised treatment. METHODS: mRNA expression profiles were obtained from GSE39754 and GSE87830, and differentially expressed mRNAs (DEmRs) between MM and controls were identified. The intersection of the two sets of DEmRs in GSE39754 and GSE87830 was identified as common mRNAs, and enrichment analysis was subsequently performed...

Piwi-interacting RNA (piRNA) targets are usually identified through base pairing between the piRNA seed region and complementary bases on the target mRNAs, which often results in false predictions. Crosslinking immunoprecipitation (CLIP) study emerges as a promising method that enables accurate identification of PIWI-clade-based targets containing RNA-binding sites. In the present study, we have analyzed the piRNA-target CLIP-seq datasets to uncover the additional characteristic features of piRNA targets. We studied important sequence and structural features using IP+ and IP- set targets that might enhance the accuracy of target site predictions...

Various studies have shown that selective molecular recognition of RNA targets by small molecules in cells, although challenging, is indeed possible. One facile strategy to enhance selectivity and potency is binding two or more sites within an RNA simultaneously with a single molecule. To simplify the identification of targets amenable to such a strategy, we informatically mined all human microRNA (miRNA) precursors to identify those with two proximal noncanonically paired sites. We selected oncogenic microRNA-27a (miR-27a) for further study as a lead molecule binds its Drosha site and a nearby internal loop, affording a homodimer that potently and specifically inhibits miR-27a processing in both breast cancer and prostate cancer cells...

BACKGROUND: Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs (ncRNAs) that silence genomic transposable elements. And researchers found out that piRNA also regulates various endogenous transcripts. However, there is no systematic understanding of the piRNA binding patterns and how piRNA targets genes. While various prediction methods have been developed for other similar ncRNAs (e.g., miRNAs), piRNA holds distinctive characteristics and requires its own computational model for binding target prediction...

MicroRNAs are implicated in the adjustment of gene expression in plant response to biotic stresses. However, the regulatory networks of transcriptome and miRNAs are still poorly understood. In the present study, we ascertained the induction of genes for small RNA biosynthesis in poplar defense to a hemibiotrophic fungus Marssonina brunnea and afterward investigated the molecular regulatory networks by performing comprehensive sequencing analysis of mRNAs and small RNAs in M. brunnea -inoculated leaves. Differentially expressed genes in M...

Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset or first recognition in the second or third trimester of pregnancy. GDM has a considerable impact on health outcomes of the mother and offspring during pregnancy, delivery, and beyond. Although the exact mechanism regarding GDM remains unclear, numerous studies have suggested that non-coding RNAs, including long non-coding (lnc)RNAs, microRNAs, and circular RNAs, were involved in the pathogenesis of GDM in which they played vital regulatory roles...

Improving biosensing performance is mandatory for biomolecular recognition and disease identification. Gold nanoparticle (GNP) based colorimetric assay is the easy and cost-effective identification method by a naked eye detection. In this research, osteosarcoma biomarker (miRNA-195) was identified by citrate-capped GNP-colorimetric assay. Since salt-induced aggregation was used to observe the color changes of GNP, sodium chloride (NaCl) and capture DNA were optimized as 50 mM and ∼20 pmol, respectively. The capture DNA only on GNP could not stable under high NaCl, and the color of GNP turned into purple...