MicroRNA in disease regulation

microRNA seedless sites attenuate strong-seed-site-mediated target repression

The paper shows that seedless miRNA binding sites reduce the effectiveness of seed site-mediated target repression in 3' UTRs, affecting miRNA-mediated gene regulation.

Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail

The paper identifies miRNAs that regulate SOAT1 expression via TGFβ pathway in avian endodermal epithelial cells during embryonic development.

Dynamics of microRNA expression during mouse prenatal development

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.

High-resolution in vivo identification of miRNA targets by Halo-Enhanced Ago2 Pulldown

This paper introduces a method to identify miRNA targets in vivo using Halo-Enhanced Ago2 Pulldown and demonstrates its application in mouse models.

Identification of Novel miRNAs in Mouse Embryonic Stem Cells, Embryonic Fibroblasts, and Reprogrammed Pluripotent Cells

The paper identifies nine novel miRNAs in mouse cells, including a species-specific miRNA with a unique evolutionary origin through inverted duplication.

Identification and comparison of genes differentially regulated by transcription factors and miRNAs

The paper identifies genes differentially regulated by transcription factors and miRNAs using TCGA data and linear models to compare their regulatory effects.

Comprehensive analysis of human microRNA-mRNA interactome

The paper analyzes human microRNA-mRNA interactions using experimental data and identifies patterns of regulation and context-dependent behavior.

HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development

This paper identifies HRPK-1 as an RNA-binding protein that interacts with miRNAs and modulates their activity during C. elegans development, enhancing miRNA-mediated gene repression.

MirGeneDB 2.0: The metazoan microRNA complement

MirGeneDB 2.0 expands curated microRNA gene annotations to 45 metazoan species, revealing many false positives and missing miRNAs in previous annotations.

Inferring disease-associated microRNAs using semi-supervised multi-label graph convolutional networks

This study introduces DimiG, a semi-supervised multi-label graph convolutional network to infer disease-miRNA associations, showing improved performance over existing methods.

Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines

The paper investigates miRNA expression changes in trophoblastic cell lines under LIF stimulation and identifies associated pathways.

Differential gene expression and functional pathway enrichment in colon cell line CCD 841 CoN (CRL-1790) transfected with miR-mimics miR-18b, miR-142-3p, miR-155, and miR-890.

The paper analyzes differential gene expression and pathway enrichment in colon cell lines transfected with specific miR-mimics, providing a resource for miRNA dysregulation effects.

The key miRNAs for metastasis and survival of colon adenocarcinoma

This study identifies two key miRNAs, has-miR-126-3p and has-miR-137, associated with metastasis and prognosis in colon adenocarcinoma using WGCNA and clinical data.

Alzheimer’s disease risk SNPs show no strong effect on miRNA expression in human lymphoblastoid cell lines

This study investigates the effect of Alzheimer's disease risk SNPs on miRNA expression in human lymphoblastoid cell lines and finds limited evidence of miRNA eQTL effects, with two notable exceptions.

Machine learning to detect Alzheimer’s disease from circulating non-coding RNAs

The paper uses machine learning to analyze circulating microRNAs and finds they can distinguish Alzheimer's patients from controls with 87.6% accuracy.

Lentivirus-mediated long-term overexpression of specific microRNA in mammalian cells

This study develops a method to achieve long-term overexpression of specific microRNAs using lentivirus vectors and demonstrates its efficiency and utility for miRNA research and therapy.

Modeling the dynamics of Let-7-coupled gene regulatory networks linking cell proliferation to malignant transformation

The paper models how Let-7 couples cell cycle and transformation gene regulatory networks, showing their mutual control and role in cancer progression and tumor heterogeneity.

SEA: The Small RNA Expression Atlas

SEA provides a web tool for querying and analyzing small RNA expression across ten organisms, including differential expression and classification comparisons.

AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis after ischemic stroke

The paper uses AGO CLIP to identify miRNA-target interactions in the brain after ischemic stroke, revealing miR-29 family members lose target regulation, leading to rapid proteomic changes in glutamate homeostasis.

miR-92a-3p controls cell cycle progression in zebrafish

The paper shows miR-92a-3p suppresses wee2 translation in zebrafish embryos, regulating cell cycle progression during early development.

Tissue-specific 3 prime end-adenylation of miR-125b mediates cell survival

The paper identifies a tissue-specific isomiR, miR-125b+A, which enhances cell survival by more potently inhibiting CASP6 expression in vascular smooth muscle cells.

Somatic mutations in miRNA genes in lung cancer - potential functional consequences of non-coding sequence variants

The paper analyzes somatic mutations in miRNA genes in lung cancer, identifying mutational hotspots and their potential functional consequences on miRNA function and target interactions.

Hsa-mir-210 as a novel signature predicts survival in lung squamous cell carcinoma using bioinformatics analysis

This study identifies hsa-mir-210 as a prognostic marker for lung squamous cell carcinoma through differential expression and survival analysis of miRNAs from TCGA and GEO datasets.

miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

miRDriver identifies copy number-derived miRNA-gene regulatory interactions in cancer using integrated genomic data and outperforms existing methods.

Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences

This study compares miRNA profiling methods using synthetic pools and exRNA samples, finding significant differences in reproducibility, accuracy, and sensitivity across platforms.

miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules

miRspongeR is an R/Bioconductor package that identifies and analyzes miRNA sponge interaction networks and modules using seven methods and an integrative approach.

Global analyses of the dynamics of mammalian microRNA metabolism

The paper measures production and degradation rates of miRNAs in different mouse cell types, revealing rapid duplex production, fast Argonaute loading, and cell-type-dependent half-lives.

MiR-218: A Molecular Switch and Potential Biomarker of Susceptibility to Stress

This study shows that miR-218 in the medial prefrontal cortex (mPFC) influences resilience or susceptibility to depression-like behaviors in mice and that its expression in blood correlates with mPFC levels.

Global identification of functional microRNA::mRNA interactions in Drosophila

The paper identifies functional miRNA::mRNA interactions in Drosophila using AGO CLIP experiments and quantifies their impact on gene expression and translation.

A learning-based framework for miRNA-disease association prediction using neural networks

The paper introduces a neural network framework, MDA-CNN, for predicting miRNA-disease and miRNA-phenotype associations, showing improved performance over existing methods.