Circular RNAs in diseases

Genome-wide, integrative analysis implicates circular RNA dysregulation in autism and the corresponding circular RNA-microRNA-mRNA regulatory axes

The paper identifies circRNA dysregulation in ASD and links it to circRNA-microRNA-mRNA regulatory networks involving ASD risk genes.

Detecting Circular RNA from High-throughput Sequence Data with de Bruijn Graph

This paper introduces circDBG, a method for detecting circular RNA using de Bruijn graphs, showing improved accuracy, efficiency, and sensitivity compared to existing methods.

The identification of mecciRNAs and their roles in mitochondrial entry of proteins

The paper identifies mecciRNAs, circular RNAs from the mitochondrial genome that assist in the mitochondrial import of nuclear-encoded proteins by acting as molecular chaperones.

ACValidator: a novel assembly-based approach for in silico validation of circular RNAs

ACValidator validates circRNAs by assembling reads around junctions and aligning contigs to detect back-spliced junctions, achieving high sensitivity and specificity in simulated and experimental datasets.

A comprehensive pipeline for accurate annotation and quantification of circRNAs

This paper introduces a comprehensive pipeline for circRNA annotation and quantification, showing improved accuracy and sensitivity over existing methods.

High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome

This study uses RNA-seq to compare circRNA expression in lesional and non-lesional psoriasis skin, finding reduced circRNA abundance without clear links to miRNA binding site changes.

Assessing circular RNAs in Alzheimer disease

The paper replicates and extends findings on circRNA expression in Alzheimer's disease, showing consistent upregulation and downregulation patterns and altered expression in related neurodegenerative conditions.

The role of SRSF3 splicing factor in generating circular RNAs

The paper investigates the role of SRSF3 in circRNA biogenesis and identifies its impact on circRNA production and potential involvement in hematologic malignancies.

A CLEAR pipeline for direct comparison of circular and linear RNA expression

The paper introduces CLEAR, a pipeline to compare circular and linear RNA expression using RNA-seq data by calculating CIRCscore.

Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation

The paper identifies circRNAs in porcine oocytes and cumulus cells, showing circARMC4 is essential for oocyte maturation and early embryo development.

Predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks

The paper introduces CRIP, a deep learning method for predicting circRNA-RBP interactions using RNA sequences, outperforming existing methods with a hybrid CNN-RNN architecture.

Identification of human genetic variants controlling circular RNA expression

The paper identifies genetic variants that control circular RNA expression by analyzing circRNA and genome sequence variation in lymphoblastoid cell lines from the 1000 Genomes Project.

Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing

Ularcirc detects and analyzes circular RNAs using a novel method to filter false positives and provides visualization tools for circRNA characterization.

The Landscape Of Circular RNA Expression In The Human Brain

The paper characterizes circRNA expression in human brain samples, identifies novel circRNAs, and finds a co-expression module upregulated in autism.

Global increase in circRNA levels in myotonic dystrophy

This study shows increased global circRNA levels in myotonic dystrophy type 1, identifies circRNAs associated with disease severity, and links circRNA levels to muscle weakness and alternative splicing changes.

Circular RNAs in the ageing African turquoise killifish

This study identifies and characterizes circRNAs in the ageing African turquoise killifish across multiple tissues and time points, providing a resource for circRNA and ageing research.

Unearthing Regulatory Axes of Breast Cancer circRNAs Networks to Find Novel Targets and Fathom Pivotal Mechanisms

This study identifies key circRNAs, RBPs, miRNAs, and mRNAs in breast cancer through systems biology approaches, revealing potential therapeutic targets and regulatory mechanisms.

Transcriptome-wide map of m6A circRNAs identified in hypoxic pulmonary hypertension rat model

This study identifies the transcriptome-wide map of m6A circRNAs in a hypoxic pulmonary hypertension rat model, showing decreased m6A levels and altered circRNA-miRNA-mRNA networks.

Non-coding AUG circRNAs constitute an abundant and conserved subclass of circles

The paper identifies and characterizes AUG circRNAs, showing they are abundant, conserved, and produced without Alu elements, but with no evidence of translation.

Dysregulation of circular RNAs in myotonic dystrophy type 1

This study identifies dysregulated circular RNAs in myotonic dystrophy type 1 patients using RNA-sequencing and qPCR, showing tissue-specific expression patterns and potential as biomarkers.

Identification of circular RNAs in porcine spermatozoa and their relation to sperm motility

This study identifies circRNAs in porcine sperm and links some to sperm motility, suggesting potential as biomarkers for male fertility.

Translation and Transforming Activity of a Circular RNA from Human Papillomavirus

This study identifies circE7, a circular RNA from HPV that is translated into E7 oncoprotein, contributing to cervical cancer progression.

BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions

BIQ indexes backsplice junctions in transcriptome datasets to query circular RNA occurrence and abundance.

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut of Apis cerana cerana workers

This study identifies circRNAs and their regulatory networks in the midgut of eastern honeybees, revealing their potential roles in midgut development through ceRNA mechanisms.

Comprehensive Assessment of Sequence and Expression of Circular-RNAs in Progenitor Cell Types of the Developing Mammalian Cortex

The paper identifies and characterizes circRNAs in developing mouse cortical progenitor cells, revealing nearly 4,000 new circRNAs and their expression patterns.

Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

The paper identifies circRNA expression profiles in intermuscular fat of lean and obese pigs, finding 809 differentially expressed circRNAs with 29 significant differences.

Genome-wide identification and functional analysis of circRNAs in Zea mays

The paper identifies and characterizes circRNAs in maize, finding conserved circRNAs across species and circRNAs involved in stress responses and gene regulation.

An in vivo knockdown strategy reveals multiple functions for circMbl

This paper develops a shRNA-based strategy to knock down circMbl in Drosophila, revealing its functional roles in development, behavior, and synaptic function.

Modeling circRNAs expression pattern with integrated sequence and epigenetic features identifies H3K79me2 as regulators for circRNAs expression

The paper introduces CIRCScan, a machine learning framework that predicts circRNA expression using sequence and epigenetic features, identifying H3K79me2 as a key regulator.

BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages

The paper investigates circRNA expression across tissues and developmental stages in rats, finding unique age-dependent patterns in testes linked to spermatogenesis.