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We report here that the expression of endogenous microRNAs (miRNAs) can be efficiently silenced in Arabidopsis thaliana (Arabidopsis) using artificial miRNA (amiRNA) technology. We demonstrate that an amiRNA designed to target a mature miRNA directs silencing against all miRNA family members, whereas an amiRNA designed to target the stem-loop region of a miRNA precursor transcript directs silencing against only the individual family member targeted. Furthermore, our results indicate that amiRNAs targeting both the mature miRNA and stem-loop sequence direct RNA silencing through cleavage of the miRNA precursor transcript, which presumably occurs in the nucleus of a plant cell during the initial stages of miRNA biogenesis. This suggests that small RNA (sRNA)-guided RNA cleavage in plants occurs not only in the cytoplasm, but also in the nucleus. Many plant miRNA gene families have been identified via sequencing and bioinformatic analysis, but, to date, only a small tranche of these have been functionally characterized due to a lack of effective forward or reverse genetic tools. Our findings therefore provide a new and powerful reverse-genetic tool for the analysis of miRNA function in plants.
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http://dx.doi.org/10.1093/mp/ssq061 | DOI Listing |
Anal Chem
September 2025
Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological and Chemical Engineering, Jiaxing University, Jiaxing 314001, China.
Despite the promise of electrochemical biosensors in amplified nucleic acid diagnostics, existing high-sensitivity platforms often rely on a multilayer surface assembly and cascade amplification confined to the electrode interface. These stepwise strategies suffer from inefficient enzyme activity, poor mass transport, and inconsistent probe orientation, which compromise the amplification efficiency, reproducibility, and practical applicability. To address these limitations, we report a programmable dual-phase electrochemical biosensing system that decouples amplification from signal transduction.
View Article and Find Full Text PDFPlant J
September 2025
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
Genome imbalance, resulting from varying the dosage of individual chromosomes (aneuploidy), has a more detrimental effect than changes in complete sets of chromosomes (haploidy/polyploidy). This imbalance is likely due to disruptions in stoichiometry and interactions among macromolecular assemblies. Previous research has shown that aneuploidy causes global modulation of protein-coding genes (PCGs), microRNAs, and transposable elements (TEs), affecting both the varied chromosome (cis-located) and unvaried genome regions (trans-located) across various taxa.
View Article and Find Full Text PDFPLoS One
September 2025
Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China.
MicroRNAs (miRNAs) are critical regulators of gene expression in cancer biology, yet their spatial dynamics within tumor microenvironments (TMEs) remain underexplored due to technical limitations in current spatial transcriptomics (ST) technologies. To address this gap, we present STmiR, a novel XGBoost-based framework for spatially resolved miRNA activity prediction. STmiR integrates bulk RNA-seq data (TCGA and CCLE) with spatial transcriptomics profiles to model nonlinear miRNA-mRNA interactions, achieving high predictive accuracy (Spearman's ρ > 0.
View Article and Find Full Text PDFPLoS One
September 2025
Department of Hepatobiliary Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
Objective: This study employs integrated network toxicology and molecular docking to investigate the molecular basis underlying 4-nonylphenol (4-NP)-mediated enhancement of breast cancer susceptibility.
Methods: We integrated data from multiple databases, including ChEMBL, STITCH, Swiss Target Prediction, GeneCards, OMIM and TTD. Core compound-disease-associated target genes were identified through Protein-Protein Interaction (PPI) network analysis.
PLoS One
September 2025
Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China.
Background: Disulfidptosis, a novel cellular death manner, has yet to be fully explored within the context of pulmonary arterial hypertension (PAH). This study aims to identify genes implicated in PAH that are involved in disulfidptosis.
Method: Based on data from the GEO database, this study employed co-expression analysis, Weighted Gene Co-Expression Network Analysis (WGCNA), hub gene identification, and Gene Set Enrichment Analysis (GSEA) to uncover genes associated with PAH and disulfidptosis.