MicroRNA in disease regulation

DraculR detects haemolysis contamination in small RNA sequencing data by calculating a haemolysis metric from microRNA expression data.

The paper investigates miRNA regulation of mRNA translation and stability using reporter genes in human cancer cells, revealing miRNA-specific effects and interactions between targeted and non-targeted transcripts.

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

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

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

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

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.

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 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.

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.

The paper identifies a switch from DICER-dependent to Argonaute-mediated miRNA biogenesis in cancer, showing that non-canonical processing of oncogenic miRNAs promotes cancer progression.

This study identifies miRNA-mRNA hub genes and natural drug candidates for lung carcinoma using in silico analysis of gene expression data and molecular docking.

The paper shows XRN2 degrades specific tumor suppressor miRNAs, affecting cancer cell behavior and patient survival.

This study examines miR-202 and trib-1 expression in HepG2 cells under metabolic and inflammatory stress, finding decreased trib-1 and increased miR-202 levels.

The paper uses EISA to distinguish post-transcriptional regulation by miRNAs from transcriptional changes in pig tissues, identifying miRNA-target interactions in muscle and adipose tissues.

The paper identifies primary miRNAs that coordinate the biogenesis of secondary miRNAs to regulate immune response in activated macrophages.

This paper identifies pqn-59 as a factor that antagonizes miRNA-mediated repression and promotes stress granule formation in C. elegans, contributing to regulatory bistability in developmental gene networks.

The paper performs an in-silico analysis of HCC omics data to show microRNAs can act as both tumor suppressors and oncomirs through complex regulatory interactions.

The paper identifies miR-2392 as a miRNA involved in SARS-CoV-2 infection, showing its role in inflammation, glycolysis, and hypoxia, and develops a miRNA-based therapeutic targeting it.

The paper systematically quantifies microRNA affinities in vivo using mouse embryonic stem cells and finds that miRNA target affinities vary widely and correlate with expression levels.

This study characterizes the endoribonuclease activity of XRN-2 in C. elegans, showing its critical role in miRNA turnover and survival of dauer worms, and its importance in rRNA maturation for translation.

The paper identifies a microRNA turnover complex in C. elegans and shows it can switch between ATP-dependent and ATP-independent modes of operation.

feamiR uses genetic algorithms to select features for predicting miRNA-mRNA interactions, improving accuracy by analyzing seed, compensatory, and flanking regions.

The paper identifies 112 miRNA combinations that accurately distinguish healthy breast tissue from breast carcinoma using a machine learning approach that generates sets of equivalent predictive models.

This study identifies 8 putative SARS-CoV-2 miRNAs and their potential human gene targets, showing down-regulation of these targets in infected samples.

This study identifies miR-375 as a key regulator of intestinal crypt homeostasis, showing its role in stem cell proliferation, tuft cell abundance, and resistance to infection and cancer.

The paper identifies key non-coding RNAs involved in fluid shear stress and reactive oxygen species-mediated colon cancer metastasis through network analysis and survival analysis.