Cell-Type Specific Features of Circular RNA Expression

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.

• Publication year

  2013

• Venue

  PLoS Genetics

• Publication date

  2013-09-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pgen.1003777PMID 24039610PMCID 3764148
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Circular RNAs are abundant, conserved, and associated with ALU repeats.

  2013influential reference
• Natural RNA circles function as efficient microRNA sponges

  2013cited by this paper
• Faculty Opinions recommendation of Natural RNA circles function as efficient microRNA sponges.

  2013cited by this paper
• Circular RNAs are a large class of animal RNAs with regulatory potency

  2013cited by this paper
• Epigenetic regulation of the 1,25-dihydroxyvitamin D3 24-hydroxylase (CYP24A1) in colon cancer cells

  2013cited by this paper
• Ambra1 at the crossroad between autophagy and cell death

  2013cited by this paper
• Marked increase of CYP24A1 mRNA level in hepatocellular carcinoma cell lines following vitamin D administration.

  2012cited by this paper
• Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

  2012influential reference
• Protection from feed-forward amplification in an amplified RNAi mechanism.

  2012cited by this paper
• Duplication of 7q36.3 encompassing the Sonic Hedgehog (SHH) gene is associated with congenital muscular hypertrophy.

  2012cited by this paper
• The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

  2012cited by this paper
• Fast gapped-read alignment with Bowtie 2

  2012cited by this paper
• Vitamin D receptor, CYP27B1 and CYP24A1 genes polymorphisms association with oral cancer risk and survival.

  2012cited by this paper
• Marked Increase in CYP24A1 Gene Expression in Human Papillary Thyroid Cancer

  2011cited by this paper
• The developmental transcriptome of Drosophila melanogaster

  2010cited by this paper
• Alterations in Vitamin D signalling and metabolic pathways in breast cancer progression: a study of VDR, CYP27B1 and CYP24A1 expression in benign and malignant breast lesions Vitamin D pathways unbalanced in breast lesions

  2010cited by this paper
• CYP24A1 splice variants--implications for the antitumorigenic actions of 1,25-(OH)2D3 in colorectal cancer.

  2010cited by this paper
• The Developmental Transcriptome of Drosophila melanogaster

  2010cited by this paper
• Coexistence of copy number increases of ZNF217 and CYP24A1 in colorectal cancers in a Chinese population.

  2010cited by this paper
• Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk

  2010cited by this paper
• CYP24A1 Is an Independent Prognostic Marker of Survival in Patients with Lung Adenocarcinoma

  2010cited by this paper
• The vitamin D/CYP24A1 story in cancer.

  2010cited by this paper
• The Candidate Oncogene CYP24A1: A Potential Biomarker for Colorectal Tumorigenesis

  2010cited by this paper
• Vitamin D Related Genes, CYP24A1 and CYP27B1, and Colon Cancer Risk

  2009cited by this paper
• Vitamin D Related Genes , CYP 24 A 1 and CYP 27 B 1 , and Colon Cancer Risk

  2009cited by this paper
• Ambra1 regulates autophagy and development of the nervous system

  2007cited by this paper
• Comprehensive Association Analysis of the Vitamin D Pathway Genes, VDR, CYP27B1, and CYP24A1, in Prostate Cancer

  2007cited by this paper
• Noncanonical RNAs from transcripts of the Drosophila muscleblind gene.

  2006cited by this paper
• Substrate Recognition and Catalysis by the Exoribonuclease RNase R*

  2006cited by this paper
• Expression of VDR and CYP24A1 mRNA in human tumors

  2005cited by this paper
• The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.

  2003cited by this paper
• Internal ribosome entry sites tests with circular mRNAs.

  1998cited by this paper
• Northern blotting of RNA denatured in glyoxal without buffer recirculation.

  1997cited by this paper
• During in vivo maturation of eukaryotic nuclear mRNA, splicing yields excised exon circles.

  1996cited by this paper
• Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping.

  1996cited by this paper
• Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs.

  1995cited by this paper
• Circular transcripts of the testis-determining gene Sry in adult mouse testis.

  1993cited by this paper
• Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells

  1979cited by this paper
• Potato spindle tuber virus: a plant virus with properties of a free nucleic acid. 3. Subcellular location of PSTV-RNA and the question of whether virions exist in extracts or in situ.

  1971cited by this paper
• Potato Spindle Tuber Virus: A Plant Virus with Properties of a Free Nucleic Acid

  1967cited by this paper

• The role of circular RNAs in the diagnosis and therapy of psoriasis

  2026cites this paper
• CircRNA-regulated programmed cell death networks in cardiomyocytes: Molecular crosstalk and therapeutic translation

  2026cites this paper
• The Interaction of CircESR1 and HNRNPAB Regulates Cell Cycle Transition of Breast Cancer Cell

  2026cites this paper
• Neuroendocrine-associated epigenetic factors in cellular senescence: mechanisms and therapeutic implications

  2026cites this paper
• The Evolution of Bees: Insights from ‘Omic Studies

  2026cites this paper
• Junction-targeting designs limit the application of CRISPR-Cas13d in circular RNA perturbation studies

  2026cites this paper
• A brain-enriched circRNA blood biomarker can predict response to SSRI antidepressants.

  2026cites this paper
• PTBP1-mediated inhibition of circular RNA SCMH1 biogenesis impairs brain recovery after ischemic stroke

  2026cites this paper
• Circ_0000190 inhibits the progression of triple negative breast cancer by regulating miR-301a/MEOX2 pathway.

  2025cites this paper
• In silico mining of banana circular RNAs in response to biotic andabiotic stress: Classification and their distribution on genome

  2025cites this paper
• N 6-methyladenosine-modified circular RNAs in aging-associated gastrointestinal tumors

  2025cites this paper
• Establishment and evaluation of a circAdpgk-0001 knockdown method using CRISPR–Cas13d RNA-targeting technology

  2025cites this paper
• Circular RNAs in Metabolic Diseases.

  2025cites this paper
• The Role of Hsa_circ_0087862/miR-149-5p/TRAF6 Regulatory Axis in Colorectal Cancer Progression

  2025cites this paper
• circ_0002970 promotes fibroblast-like synoviocytes invasion and the inflammatory response through Hippo/YAP signaling to induce CTGF/CCN1 expression in rheumatoid arthritis

  2025cites this paper
• Biogenesis and function of circular RNAs and their implications in the Down syndrome brain

  2025cites this paper
• Protocol for mouse brain tissue processing and downstream analysis of circRNA-protein interactions in vivo

  2025cites this paper
• Formation of Circular RNAs.

  2025cites this paper
• Integration of Short- and Long-Read RNA Sequencing Enables the Discovery of Circular RNAs.

  2025cites this paper
• Challenges and Future Prospectives in Circular RNA Investigation.

  2025cites this paper
• Emerging roles and therapeutic potential of non-coding RNA in osteosarcoma: a review

  2025cites this paper
• Circular RNAs at the crossroads of acute pancreatitis: bridging molecular mechanisms to diagnostic and therapeutic innovations

  2025cites this paper
• Circular RNAs as Biomarkers and Therapeutic Targets in Diabetic Cardiovascular Complications

  2025cites this paper
• Deciphering the multifaceted role of circular RNA in aging: from molecular mechanisms to therapeutic potentials

  2025cites this paper
• circRNA/TLR interaction: key players in immune regulation and autoimmune diseases

  2025cites this paper
• Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities

  2025cites this paper
• N6‐Methyladenosine‐Modified circNEK11 Promotes Hepatocellular Carcinoma Progression via the miR‐1236‐3p/GPX2 Axis

  2025cites this paper
• Circular RNAs and Cancers.

  2025cites this paper
• Hsa_circ_0018909 promotes non-small cell lung cancer by directly regulating hsa-miR-513b-5p

  2025cites this paper
• Novel insights into the N 6-methyladenosine modification on circRNA in cancer

  2025cites this paper
• Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity

  2025cites this paper
• A versatile toolbox for determining IRES activity in cells and embryonic tissues

  2025cites this paper
• Role of circular RNAs in cancer therapy resistance

  2025cites this paper
• Dysregulated Circular RNA and Long non-coding RNA-Mediated Regulatory Competing Endogenous RNA Networks (ceRNETs) in Ovarian and Cervical Cancers: A Non-coding RNA-Mediated Mechanism of Chemotherapeutic Resistance with New Emerging Clinical Capacities.

  2025cites this paper
• Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators

  2025cites this paper
• Circular RNAs modulate cell death in cardiovascular diseases

  2025cites this paper
• Circular RNA profiling revealed an evolutionarily conserved circACACA promotes liver lipid metabolism, oxidative stress, and autophagy disorder in a ceRNA manner

  2025cites this paper
• EXPRESS: Understanding the correlation of IL-6 with CircRNA-DLGAP4 in the pathogenesis and diagnosis of Rheumatoid Arthritis.

  2025cites this paper
• Reference-guided detection of the transcriptome reveals circular RNA-related competing endogenous RNA networks in response to three respiration pathogens in pig lungs

  2025cites this paper
• N6-methyladenosine-modified circDCP2 promotes carbon black nanoparticle-induced malignancy in human bronchial epithelial cells via PI3K-AKT pathway and macrophage homeostasis

  2025cites this paper
• Circular RNA RORβ regulates TGFβR1 in alcohol-induced fibroblast-to-myofibroblast differentiation

  2025cites this paper
• Circular RNAs Regulate Transcription and Translation.

  2025cites this paper
• AQUARIUM_HB: a bioinformatics pipeline for human blood circular RNA analysis

  2025cites this paper
• Nucleic acid-encoded antibody gene transfer-next generation of antibody therapies

  2025cites this paper
• CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration

  2025cites this paper
• Role of non-coding RNAs in radiotherapy sensitivity in non-small cell lung cancer

  2025cites this paper
• Circular RNA circMYBL2 regulates the progression of ovarian cancer through miR-195-5P/BIRC5 axis

  2025cites this paper
• The role of circular RNAs in autoimmune diseases: Potential diagnostic biomarkers and therapeutic targets

  2025cites this paper
• RNA methylation modifications in neurodegenerative diseases: Focus on their enzyme system

  2025cites this paper
• Circular RNAs in cancer

  2025cites this paper
• CircTHADA regulates endothelial cell pyroptosis in diabetic retinopathy through miR-494-3p/CASP1/GSDMD-N/IL-1β pathway.

  2025cites this paper
• Presence of Alzheimer's disease variants in circular RNA of PSEN1 and PSEN2

  2025cites this paper
• Circular RNA FCHO2 promotes airway remodeling in COPD via regulating nuclear translocation of PTBP1 to repress the splicing of GRN pre-mRNA

  2025cites this paper
• Abiotic stress-induced circular RNAs: Implications for plant stress tolerance.

  2025cites this paper
• Research Progress on circRNA in Renal Cell Carcinoma (RCC): Biogenesis, Biological Functions, and Clinical Significance

  2025cites this paper
• Role of Non-Coding RNAs in Acute Myeloid Leukemia

  2025cites this paper
• Circular RNAs Binding to RNA-Binding Proteins.

  2025cites this paper
• An Overview of Circular RNAs.

  2025cites this paper
• Circular RNAs: A Potential Regulator in Environmental Chemical Carcinogenesis.

  2025cites this paper
• Circular RNAs in cardiovascular disease: A paradigm shift in diagnosis and therapeutics.

  2025cites this paper
• Down-regulation of circMUC16 inhibited the progression of ALL via interaction with miR-1182 and TPPP3

  2025cites this paper
• Assessment of Non-Coding RNAs (miR-506 and circRNA 000284) and their Target Gene SNAIL-2 in Breast Tumors: Implications for Prognosis and a Possible Circulating Biomarker

  2025cites this paper
• Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

  2025cites this paper
• Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.

  2025cites this paper
• Recent advances in the regulatory and non-coding RNA biology of osteogenic differentiation: biological functions and significance for bone healing

  2025cites this paper
• Circular RNAs in cancer stem cells: Insights into their roles and mechanisms (Review)

  2025cites this paper
• Circular RNAs increase during vascular cell differentiation and are biomarkers for vascular disease

  2025cites this paper
• Degradation of circular RNA by the ribonuclease DIS3.

  2025cites this paper
• Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses

  2025cites this paper
• Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene

  2025cites this paper
• ADAR1‐HNRNPL‐Mediated CircCANX Decline Promotes Autophagy in Chronic Obstructive Pulmonary Disease

  2025cites this paper
• A Novel Protein NAB1‐356 Encoded by circRNA circNAB1 Mitigates Atrial Fibrillation by Reducing Inflammation and Fibrosis

  2025cites this paper
• Circular RNA discovery with emerging sequencing and deep learning technologies

  2025cites this paper
• Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies

  2024cites this paper
• MicroRNA-155 and its exosomal form: Small pieces in the gastrointestinal cancers puzzle

  2024cites this paper
• Scalable and unsupervised discovery from raw sequencing reads using SPLASH2

  2024cites this paper
• A systematic analysis of circRNAs in subnuclear compartments

  2024cites this paper
• Circular RNAs in human diseases

  2024cites this paper
• CircZMYM2 plays a pivotal role in osteosarcoma by regulating the translation of NACA and ARPC1B

  2024cites this paper
• Back to the Origin: Mechanisms of circRNA-Directed Regulation of Host Genes in Human Disease

  2024cites this paper
• MSTCRB: Predicting circRNA-RBP interaction by extracting multi-scale features based on transformer and attention mechanism.

  2024cites this paper
• Adipocytes promote metastasis of breast cancer by attenuating the FOXO1 effects and regulating copper homeostasis

  2024cites this paper
• HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes

  2024cites this paper
• Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators

  2024cites this paper
• Exosomal CircRNAs: A Future Star in Colorectal Cancer.

  2024cites this paper
• CircRNA as an Achilles heel of cancer: characterization, biomarker and therapeutic modalities

  2024cites this paper
• PlantCircRNA: a comprehensive database for plant circular RNAs

  2024cites this paper
• Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants

  2024cites this paper
• The multifaceted roles of circular RNAs in cancer hallmarks: From mechanisms to clinical implications

  2024influential citation
• Circ_BBS9 as an early diagnostic biomarker for lung adenocarcinoma: direct interaction with IFIT3 in the modulation of tumor immune microenvironment

  2024cites this paper
• Role of circular RNAs in preeclampsia (Review)

  2024cites this paper
• The circular RNA circ_0001742 regulates colorectal carcinoma proliferation and migration via the MicroRNA-431-5p/ALG8 axis

  2024cites this paper
• ESRP1-mediated biogenesis of circPTPN12 inhibits hepatocellular carcinoma progression by PDLIM2/ NF-κB pathway

  2024cites this paper
• Exploring the Roles of m6A-Modified circRNAs in Myasthenia Gravis Based on Multi-Omics Analysis

  2024cites this paper
• Imaging and quantification of human and viral circular RNAs

  2024cites this paper
• RUNX1, FUS, and ELAVL1-induced circPTPN22 promote gastric cancer cell proliferation, migration, and invasion through miR-6788-5p/PAK1 axis-mediated autophagy

  2024cites this paper
• CircRNAs in Pancreatic Cancer: New Tools for Target Identification and Therapeutic Intervention

  2024cites this paper
• Circular RNA hsa_circ_0002268 (PHACTR1) Is Specific to Gestational Diabetes Mellitus in a Polish Pregnant Population

  2024cites this paper
• Knockdown of hsa_circ_0102231 Impedes the Progression of Liver Cancer through the miR-873-SOX4 Axis.

  2024cites this paper
• Unveiling the hidden players: noncoding RNAs orchestrating polyamine metabolism in disease

  2024cites this paper