MicroRNA in disease regulation

scanMiR predicts microRNA targets using a biochemical model and k-mer affinity, offering tools for binding site scanning, affinity estimation, and repression prediction.

This paper introduces chimeric eCLIP, a method to efficiently profile miRNA:mRNA interactions at scale, showing significant improvements in recovery and specificity.

This study shows that miR-9a regulates rhomboid mRNA and protein levels in Drosophila embryos by promoting mRNA degradation and inhibiting translation.

The paper identifies the RPAP3-TRBP interaction and shows the HSP90/R2TP chaperone complex's role in dsRNA pathways by binding TRBP and affecting AGO and Dicer function.

The paper investigates how endogenous pancreatic microRNAs differentially target SARS-CoV-2 variants (Delta, Omicron, Wuhan) and upregulate diabetes-associated genes despite UTR mutations.

This study benchmarks small RNA-sequencing methods for miRNA quantification in biofluids, finding no single method outperforms others and highlighting protocol-specific biases.

The paper shows miR-10b interacts with U6 snRNA, altering splicing and affecting cell viability through changes in CDC42 isoforms and levels.

The paper curates a comprehensive reference of miRNA expression across 196 human primary cell types using public datasets and provides access through a UCSC Genome Browser track and R/Bioconductor package.

The paper presents M3Cs, a curated resource of miRNA studies in pediatric cancers, linking research to clinical and drug domains through data-driven approaches.

The paper identifies six miRNAs over-expressed in metastatic cervical cancer and suggests they could serve as diagnostic and prognostic biomarkers.

This study shows that TUT4/7 regulate miRNA variants in a cell-type-specific manner, affecting cancer cell properties and miRNA-mRNA networks.

The paper quantifies synergistic and competitive miRNA interactions using multivariate information measurement, finding that neighboring and overlapping binding sites on mRNA lead to synergistic and competitive effects, respectively.

The paper identifies miR-320a as a regulator of the unfolded protein response by analyzing TSS-miRNA targets in colorectal cancer cells using AGO-qCLASH.

The paper shows isomiRs significantly affect differential expression analysis and highlights the need to consider them instead of relying solely on reference miRNA sequences.

The paper identifies rare, highly abundant miRNAs in mammalian oocytes that resist dilution and efficiently suppress gene expression, supporting the stoichiometric hypothesis.

The paper introduces CSmiR, a method to identify cell-specific miRNA-mRNA regulatory networks using single-cell co-sequencing data, revealing unique miRNA regulation in individual cells.

The paper identifies five miRNAs associated with bone mineral density in healthy adult baboons, suggesting their role in normal aging and potential disease mechanisms.

The paper analyzes RNA-seq data from zebrafish to study miRNA arm switching during development, identifying patterns linked to gene regulation and isomiR roles in differential arm usage.

The paper introduces MapToCleave, a method to profile miRNA biogenesis in living cells, showing that stable lower basal stems enhance processing and expression across species.

The paper identifies five diabetes-associated genes upregulated in SARS-CoV-2-infected pancreatic tissue and hypothesizes that miRNA competition between viral and host genes contributes to diabetes exacerbation in COVID-19.

This paper provides a practical guide on using miRDeep2 in Galaxy to analyze miRNAs from RNA-seq data and process its output for downstream analysis.

This paper identifies therapeutic miRNA cocktails for Ewing Sarcoma using a network science-based approach to prioritize miRNA targets and combinations.

This study reviews literature and performs in silico analysis to evaluate miR-124's role in neurodegenerative diseases, finding it reduces inflammation and apoptosis by targeting NF-kb and BACE1.

The paper identifies RNaseP as essential for processing 5-tailed mirtrons and links their biogenesis to tRNA fragment accumulation.

The paper alters miR-140-5p and -3p stoichiometry in mice to identify their physiological targets and roles in bone development.

miRbiom uses Bayesian causal networks of RBP-miRNA interactions to predict miRNA profiles with high accuracy without requiring separate miRNA profiling experiments.

The paper shows that microRNA-182/microRNA-183 repress Ago2 to maintain pluripotency in mESCs, revealing a regulatory circuit involving microRNA machinery.

The paper identifies that only 6% of expressed genes are functionally regulated by miRNAs in mESCs using integrative analysis of transcriptome data and miRNA interaction predictions.

CancerMIRNome provides an interactive database for analyzing and visualizing miRNA expression data from cancer studies to identify dysregulated miRNAs and develop biomarkers.

This study develops a genetic tool to reversibly inhibit miRNA-mediated gene repression in vivo and shows tissue-specific dependencies on miRNA function for homeostasis and regeneration.