Circular RNAs in diseases

Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts

This study shows that circRNA overexpression can produce false translation signals from linear RNA byproducts, highlighting the need for rigorous controls in circRNA research.

JEDI: Circular RNA Prediction based on Junction Encoders and Deep Interaction among Splice Sites

JEDI predicts circular RNA from nucleotide sequences using attention mechanisms and cross-attention layers, outperforming existing methods and enabling backsplicing hotspot discovery.

Targeting circPTPN12/1 miR-21-5p/ΔNp63α pathway as a therapeutic strategy for human endometrial fibrosis

The paper identifies circPTPN12 as a regulator of miR-21-5p and ΔNp63α in endometrial fibrosis, suggesting it as a therapeutic target.

Regulation of circular RNA circNFATc3 in cancer cells alters proliferation, migration and oxidative phosphorylation

This study shows that circNFATc3 affects cancer cell proliferation, migration, and oxidative phosphorylation through gain and loss of function experiments.

riboCIRC: a comprehensive database of translatable circRNAs

riboCIRC provides a database of translatable circRNAs with computational predictions, experimental validations, and cross-species conservation analysis.

DEBKS: A Tool to Detect Differentially Expressed Circular RNA

DEBKS detects differentially expressed circular RNAs by analyzing back-splicing events in RNA-seq data, showing efficiency and accuracy through real and simulated data.

CircRNA may not be "circular"

The paper investigates circRNA structure and function, finding internal complementary base-pairing sequences and proposing an 'open-close effect' hypothesis for circRNA transitions.

Signal and noise in circRNA translation

The paper discusses the challenges of distinguishing circRNA translation signal from noise and outlines experimental guidelines for studying circRNA translation.

CircTulp4 functions in Alzheimer's disease pathogenesis by regulating its parental gene, Tulp4

The paper identifies circTulp4 as a circRNA that regulates its parental gene Tulp4, affecting nervous system function and potentially contributing to Alzheimer's disease pathogenesis.

The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis

This study identifies SFPQ as a key regulator of circRNA biogenesis by maintaining long-intron splicing and preventing aberrant splicing events.

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying essential circRNAs

This study compares shRNA and CRISPR/Cas13d screens for circRNA function, finding that optimized CRISPR/Cas13d reduces false positives and identifies true functional circRNAs.

Prognostic significance of circRNAs expression in breast carcinoma patients: A meta-analysis

This study performs a meta-analysis to assess the prognostic significance of circRNAs in breast cancer, identifying 28 circRNAs associated with survival outcomes.

A genome-wide circular RNA transcriptome in Rat

The paper identifies and characterizes circular RNAs in rat using multiple computational pipelines and validates some candidates through experimental methods.

Human Polyomavirus-Encoded Circular RNAs

This study identifies circular RNAs encoded by human polyomaviruses that produce proteins and may contribute to viral pathogenesis.

Screening for functional circular RNAs using the CRISPR-Cas13 system

This study uses CRISPR-Cas13 to functionally screen circRNAs, identifying roles in cell growth and development.

Transcriptome-wide profiles of circular RNA and RNA binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

The paper identifies circRNA-RBP interactions in cancer, showing their role in circRNA biogenesis and cancer gene expression, with implications for bladder cancer prognosis.

circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiation

The paper identifies circZNF827 as a repressor of neuronal differentiation by forming a transcription-inhibitory complex with hnRNP-K/L proteins and modulating NGFR expression.

Circular RNA as a potential biomarker for forensic age prediction using multiple machine learning models: A preliminary study

This study explores circRNAs as age prediction biomarkers using machine learning models in forensic contexts, identifying 7 circRNAs with high predictive accuracy.

CircGLCE alleviates intervertebral disc degeneration by regulating apoptosis and matrix degradation through the targeting of miR-587/STAP1

This study identifies CircGLCE as a regulator of intervertebral disc degeneration by modulating apoptosis and matrix degradation via miR-587/STAP1.

Deciphering the mechanism underlying circRNA-mediated immune responses of western honeybees to Nosema ceranae infection

This paper identifies differentially expressed circRNAs in western honeybees infected with Nosema ceranae and links them to immune-related pathways and miRNA-mRNA interactions.

The role of Aβ circRNA in Alzheimer's disease: alternative mechanism of Aβ biogenesis from Aβ circRNA translation

This study identifies a circular RNA, circAβ-a, that translates into Aβ175, which is processed into Aβ peptides, revealing an alternative pathway for Aβ biogenesis in Alzheimer's disease.

Expression Profile of Circular RNAs in Epicardial Adipose Tissue in Heart Failure

The paper identifies circRNA expression patterns in human epicardial adipose tissue (EAT) from heart failure and non-heart failure groups, finding hsa_circ_0005565 associated with metabolic processes and insulin resistance.

An in vivo strategy for knockdown of circular RNAs

This paper describes a method to specifically knock down circRNAs in vivo and shows that circRNA downregulation affects fly development and transcriptome.

Linking the association between circRNAs and Alzheimer's disease progression by multi-tissue circular RNA characterization

The paper identifies differentially expressed circRNAs in AD brain regions and links their expression patterns to disease severity and pathways.

Biosynthesis of Circular RNA ciRS-7/CDR1as Is Mediated by Mammalian-Wide Interspersed Repeats (MIRs)

The paper identifies mammalian-wide interspersed repeats (MIRs) as facilitators of ciRS-7 circular RNA biosynthesis, revealing a new mechanism for circRNA formation.

Rcirc: an R package for circRNA analyses and visualization

Rcirc is an R package that provides downstream analysis and visualization of circRNA data, including coding ability assessment and automated visualization features.

GCNCDA: A New Method for Predicting CircRNA-Disease Associations Based on Graph Convolutional Network Algorithm

GCNCDA predicts circRNA-disease associations using a graph convolutional network, achieving high accuracy and confirming predictions with literature.

HBV pgRNA can generate a circRNA with two junction sites

The paper identifies a novel circRNA, HBV_circ_1, generated from HBV pgRNA with two junction sites in HepG2.2.15 cells and HCC tissue.

Reference-free and de novo Identification of Circular RNAs

The paper introduces a reference-free method, Cirit, for de novo detection of circRNAs from NGS transcriptomes, identifying 28,813 human circRNAs and highlighting their diverse expression patterns and splicing mechanisms.

Small circRNAs with self-cleaving ribozymes are frequently expressed in metazoan transcriptomes

The paper identifies small circRNAs with self-cleaving ribozymes in metazoan transcriptomes and shows their biosynthesis involves tRNA ligases.