miRNA target recognition identification

MicroRNAs (miRNAs) play indispensable roles in post-transcriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA-mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA-mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clamp-enhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines...

Ticks are an important type of pathogen transmission vector, and pathogens not only cause serious harm to livestock but can also infect humans. Because of the roles that ticks play in disease transmission, reducing tick pathogen infectivity has become increasingly important and requires the identification and characterization of these pathogens and their interaction mechanisms. In this study, we determined the miRNA expression profile of Hemaphysalis longicornis infected with Theileria orientalis , predicted the target genes of miRNAs involved in this infection process, and investigated the role of miRNA target recognition during host-pathogen interactions...

The DNA-based logic circuit, constructed to mimic biochemical reaction networks, is highly significant in detecting biomarkers at the molecular level. The differences in the expression levels of microRNAs (miRNAs) within different types of cells provide hope for distinguishing cell subtypes. However, reliance on a single miRNA often leads to unreliable results. Herein, we constructed an enzyme-triggered cascade logic circuit based on the AND gate, which is capable of generating corresponding fluorescence signals in the presence of target miRNAs...

Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile arthritis, accompanied by cytokine storm and hemophagocytosis. In addition, COVID-19-related hyperinflammation shares clinical features of MAS. Mechanisms that activate macrophages in MAS remain unclear. Here, we identify the role of miRNA in increased phagocytosis and interleukin-12 (IL-12) production by macrophages in a murine model of MAS. MAS significantly increased F4/80+ macrophages and phagocytosis in the mouse liver...

MicroRNAs (miRNAs) have emerged as biomarkers for the diagnosis and prognosis of various diseases, such as cancer. Recent advancements in CRISPR/Cas12a-based biosensors in combination with hybridization chain reaction (HCR) make it a promising approach for miRNA detection. To increase the compatibility of HCR and CRISPR/Cas12a, we compared two design strategies of hairpin DNA in HCR. The results showed that different arrangements of the protospacer sequence and protospacer adjacent motif (PAM) in the hairpin DNA could affect the sensing performance...

MicroRNAs (miRNAs) have significant regulatory functions in the modulation of gene expression, making them essential biomarkers for the diagnosis and prognosis of diseases. Nevertheless, the identification of miRNA poses significant difficulty in terms of its low abundance, necessitating sensitive and reliable approaches. Herein, we develop a simple approach, termed C atalytic assembly of D NAzyme i ntegrates with P rimer E xchange R eaction (CDiPER), for reliable and sensitive miRNA detection through the target recognition-triggered DNAzyme assembly and primer exchange reaction (PER) strategy...

Inspired by the programmability and modifiability of nucleic acids, point-of-care (POC) diagnostics for nucleic acid target detection is evolving to become more diversified and intelligent. In this study, we introduce a fluorescent and photothermal dual-mode logic biosensing platform that integrates catalytic hairpin assembly (CHA), toehold-mediated stand displacement reaction (SDR) and a DNA walking machine. Dual identification and signal reporting modules are incorporated into DNA circuits, orchestrated by an AND Boolean logic gate operator and magnetic beads (MBs)...

UNLABELLED: Pseudouridylation, the conversion of uridine (U) to pseudouridine (Ѱ), is one of the most prevalent and evolutionary conserved RNA modifications, which is catalyzed by pseudouridine synthase (PUS) enzymes. Ѱs play a crucial epitranscriptomic role by regulating attributes of cellular RNAs across diverse organisms. However, the precise biological functions of PUSs in plants remain largely elusive. In this study, we identified and characterized 21 members in the rice PUS family which were categorized into six distinct subfamilies, with RluA and TruA emerging as the most extensive...

OBJECTIVE: Ulcerative colitis (UC) is an inflammatory disease characterized by recurrent episodes of chronic intestinal inflammation. It is closely associated with immune dysregulation in the intestines. However, the mechanisms underlying the role of immune-related N7-methylguanosine (m7G) internal modification in UC remain unclear. METHODS: We conducted a screening of differentially expressed genes (DEGs) associated with m7G and performed immune infiltration analysis...

False positive which is mostly caused by the nonspecific amplification has severely hindered the development of nucleic acid detection and it is hard to avoid. Therefore, specific signals recognition and output in nucleic acid amplification are crucial to reliability of clinical diagnosis. Herein, we proposed a one-step and rapid miRNA detection strategy with specific signal identification, dual amplification and output. And this strategy was named as high-temperature hybridization chain reaction coupled with strand displacement amplification (HSA)...

MicroRNAs (miRNAs) are small RNA molecules that can play important roles as diagnostic/prognostic biomarkers and therapeutic targets for cancers and other diseases. Herein, an identification-cleavage-amplification (ICA) strategy for highly sensitive and versatile detection of miRNA has been proposed, and successfully applied to miR-155 and miR-21 assays. It combines an aligner-target mediated cleavage with strand displacement amplification (ATMC-SDA) to achieve the ICA process. During the identification process, a DNA-aligner (DA) and a DNA-amplicon (DM) can bind together with the help of target miRNA, forming a T-junction structure...

The brown planthopper (BPH) is the most serious pest causing yield losses in rice. MicroRNAs (miRNAs) are emerging as key modulators of plant-pest interactions. In the study, we found that osa-miR162a is induced in response to BPH attack in the seedling stage and tunes rice resistance to the BPH via the α-linolenic acid metabolism pathway as indicated by gas chromatography/liquid chromatography-mass spectrometry analysis. Overexpression of osa-miR162a inhibited the development and growth of the BPH and simultaneously reduced the release of 3-hexenal and 3-hexen-1-ol to block host recognition in the BPH...

The development and performance of a DNA probe adsorbing Mn2+ -modified black phosphorus (BP@Mn2+ /DNA) hybrid nanosensor is reported that enables rapid detection of cancer-derived exosomal microRNAs (miRNAs) and exosomes. This two-dimensional (2D) nanosensor can spontaneously penetrate the lipid bilayer of exosome membranes owing to its ultra-thin geometry. Subsequently, the adsorbed probe specifically hybridizes with the target miRNA and then dissociates from the nanosensor surface, generating fluorescent signals...

MicroRNAs (miRNAs) in tumor-derived extracellular vesicles (tEVs) are important cancer biomarkers for cancer screening and early diagnosis. Multiplex detection of miRNAs in tEVs facilitates accurate diagnosis but remains a challenge. Herein, we propose an encoded fusion strategy to profile the miRNA signature in tEVs for pancreatic cancer diagnosis. A panel of encoded-targeted-fusion beads was fabricated for the selective recognition and fusion of tEVs, with the turn-on fluorescence signals of molecule beacons for miRNA quantification and barcode signals for miRNA identification using readily accessible flow cytometers...

MicroRNA (miRNA), as a kind of small non-coding ribonucleic acid (RNA) that plays a crucial role in regulating transcriptional activities, is a potential biomarker for EC diagnosis. However, reliable detection of miRNA remains a huge challenge, especially for these methods that require multiple probes for signal amplifications, due to the detective deviation caused by variation of probe concentrations. Herein, we present a novel approach for miRNA-205 identification and quantification by employing simply a ternary hairpin probe (TH probe)...

Post-transcriptional regulators, microRNAs (miRNAs), are involved in the occurrence and progression of various diseases. However, due to the complexity of disease-related miRNA regulatory networks, the typing and identification of miRNAs have remained challenging. Herein, a linear ladder-like DNA nanoarchitecture (LDN) was constructed to promote the movement efficiency of the tripedal DNA walker (T-walker), which was combined with the DNA-based logic gates and the PTCDA@PDA/CdS/WO3 photoelectrode to develop a novel biosensor for the detection of dual-miRNAs...

Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This driver diversity produces novel morphological features and clinical behaviour that serendipitously makes PBC an excellent metastasis model. Here, we report that some transfer RNA-derived small RNAs termed tRNA fragments (tRFs) perform as a constitutive tumour suppressor mechanism by blunting a potential pro-metastatic protein-RNA interaction. This mechanism is reduced in PBC progression with a gradual loss of tRNAGlyTCC cleavage into 5' end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade patient tumours...

Non-O1 Vibrio cholerae, a member of the Vibrio family, could cause gastrointestinal infection of Macrobrachium rosenbergii and result in significant economic losses. However, few studies on microRNA immunity related to non-O1 V. cholerae infection of M. rosenbergii. The aim of this study was to elucidate the mechanism of miRNA in the potential immune response of M. rosenbergii. to non-O1 V. cholerae MSVC-GY01 infection by transcriptome sequencing. Following quality screening, the control group received 10,616,712 clean reads, whereas the infected group received 9,727,616...

Although DNA nanotechnology is a promising option for fluorescent biosensors to perform bioimaging, the uncontrollable target identification during biological delivery and the spatially free molecular collision of nucleic acids may cause unsatisfactory imaging precision and sensitivity, respectively. Aiming at solving these challenges, we herein integrate some productive notions. On the one hand, the target recognition component is inserted with a photocleavage bond and a core-shell structured upconversion nanoparticle with a low thermal effect is further employed to act as the ultraviolet light generation source, under which a precise near-infrared photocontrolled sensing is achieved through a simple external 808 nm light irradiation...

Gout is a disease caused by uric acid (UA) accumulation in the joints, causing inflammation. Two UA forms - monosodium urate (MSU) and soluble uric acid (sUA) have been shown to interact physically with inflammasomes, especially with the nod-like receptor (NLR) family pyrin domain containing 3 (NLRP3), albeit the role of the immune response to UA is poorly understood, given that asymptomatic hyperuricemia does also exist. Macrophage phagocytosis of UA activate NLRP3, lead to cytokines release, and ultimately, lead to chemoattract neutrophils and lymphocytes to the gout flare joint spot...