Circular RNAs in diseases

Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism

This study identifies 3,447 circRNAs in Camelina sativa, showing their association with lipid metabolism and regulation of gene expression through alternative splicing and miRNA interactions.

Circular RNA - circCLIP2 is predominantly expressed in GSC niche and enhances glioblastoma aggressiveness via EMT and ECM signaling

This study identifies circCLIP2 as a circRNA overexpressed in glioblastoma stem cells that promotes tumor aggressiveness through EMT and ECM signaling.

Systematic screen of RNA binding proteins that enhance circular RNA translation

The paper systematically screens RNA binding proteins that enhance circular RNA translation and identifies 68 activators, using a machine learning algorithm to predict additional candidates.

Circular RNA AEBP2: A novel regulator in dendritic cell development

This study identifies circAEBP2 as a regulator of dendritic cell development and function, showing its role in promoting maturation and immune activation through interactions with hnRNP F and the NF-κB pathway.

Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing

The paper identifies circASH1L(4,5) as a protector of miR-129-5p from degradation, enhancing its stability and function in human skin wound healing.

Accurate Assembly of Circular RNAs with TERRACE

TERRACE improves circRNA assembly accuracy by using a splice graph and dynamic programming, outperforming existing methods in sensitivity and precision.

CircSMAD3 represses VSMC phenotype switching and neointima formation via promoting hnRNPA1 ubiquitination degradation

This study identifies circSMAD3 as a regulator that suppresses vascular smooth muscle cell proliferation and neointima formation by promoting hnRNPA1 degradation.

KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-disease Association Prediction

KGRACDA predicts circRNA-disease associations by capturing local depth information in a knowledge graph, outperforming existing methods.

CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs

The paper introduces CircCNNs, a CNN framework that identifies back splicing motifs in circRNA biogenesis with high specificity and reduced false positives.

Systematic loss of function screens identify pathway specific functional circular RNAs

The paper identifies pathway-specific functional circular RNAs through loss-of-function screens in cancer cell lines, revealing roles in ferroptosis, WNT, and MAPK signaling.

Unbiased and comprehensive identification of viral encoded circular RNAs in a large range of viral species and families

The paper introduces vCircTrappist, a bioinformatic pipeline for identifying viral-encoded circular RNAs, and validates its effectiveness using multiple viral families.

Glucose-regulated circular RNA Rabep1 regulates pancreatic beta-cell growth by modulating miR-335-3p/PTEN axis

The paper identifies glucose-regulated circRNAs in pancreatic β-cells, showing circRabep1 modulates β-cell growth via the miR-335-3p/PTEN axis.

ELAV mediates circular RNA biogenesis in neurons

This study shows ELAV regulates neuronal circRNA production by modulating splicing to favor circularization over linear splicing.

Tormentor: An obelisk prediction and annotation pipeline

Tormentor identifies and annotates Obelisks, circular RNA viroid-like elements found in human gut samples, using RNA-Seq data analysis.

Polyadenylated RNA sequencing analysis helps establish a reliable catalog of circular RNAs - a bovine example.

This study identifies reliable circular RNAs in bovine tissues by comparing total-RNAseq and mRNAseq data, revealing many artificial circRNAs and false entries in existing catalogs.

Bioinformatics Analysis of the Potentially Functional circRNA-miRNA-mRNA Network in Breast Cancer

This study identifies a circRNA-miRNA-mRNA network in breast cancer, highlighting potential biomarkers for basal-like breast cancer classification.

Analytical Methods and Platforms for circRNA Vector Engineering to Improve Circularization Efficiency

The paper describes analytical methods for improving circRNA circularization efficiency through vector engineering and ribozyme optimization.

Role of non-coding RNA hsa_circ_0001495 in 16HBE cellular inflammation induced by PM2.5 and O3 combined exposure

This study investigates the role of hsa_circ_0001495 in 16HBE cell inflammation caused by combined PM2.5 and O3 exposure, finding it inhibits the inflammatory response.

Hsa_circ_0001304 promotes vascular smooth muscle cell autophagy and neointimal hyperplasia through the YTHDF2/mTOR axis

This study identifies hsa_circ_0001304 as a regulator of VSMC autophagy via the miR-636/YTHDF2/mTOR axis, which promotes neointimal hyperplasia.

CircRNA-Pro: A Novel Toolkit for High-Precision Detection of Differentially Expressed Circular RNAs and Translatable Circular RNAs

CircRNA-Pro detects differentially expressed and translatable circRNAs using integrated algorithms and validation against databases, validated on breast cancer and SARS-CoV-2 datasets.

ciRS-7 and miR7 regulate ischemia induced neuronal death via glutamatergic signaling

The paper shows that ciRS-7 and miR-7 regulate ischemia-induced neuronal death through glutamatergic signaling in mice.

Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene

This study identifies and characterizes multiple circRNAs from the Drosophila scro gene, showing their biogenesis depends on intronic complementary sequences and highlighting Scro's role in regulating both linear and circular RNA production.

Decoding protein binding landscape on circular RNAs with base-resolution Transformer models

The paper introduces CircSite, a deep learning tool that predicts RBP binding sites on circRNAs at single-nucleotide resolution and identifies key binding subsequences.

Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks.

Cirscan identifies differentially active circRNA sponge mechanisms and visualizes circRNA-miRNA-mRNA networks from transcriptomic data.

Influence of FTDP-17 mutants on circTau RNAs

This study shows that FTDP-17 mutations affect circTau RNA formation and translation, with ADAR1-p150 editing playing a key role in their expression and function.

m6A-dependent circular RNA formation mediatestau-induced neurotoxicity

The paper identifies m6A-dependent circRNA dysregulation as a causal factor in tau-induced neurotoxicity using Drosophila and iPSC models.

circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA

This paper identifies circHIPK3 as a competing endogenous RNA that sequesters IGF2BP2 to regulate target mRNAs, including STAT3, and shows its correlation with bladder cancer survival.

TCCIA: A Comprehensive Resource for Exploring CircRNA in Cancer Immunotherapy

TCCIA integrates circRNA profiles, immunotherapy response data, and clinical outcomes to explore circRNA roles in cancer immunotherapy.

Versatile toolkit for highly-efficient and scarless overexpression of circular RNAs

The paper introduces a toolkit for efficiently and scarlessly overexpressing circular RNAs by redesigning plasmid vectors to eliminate molecular scars at back-splice junctions.

COL,a pipeline for identifying putatively functional back-splicing

The paper introduces COL, a computational pipeline that identifies putatively functional back-splicing events by integrating three features, achieving lower false positive rates than existing methods.