ArticleBMC genomics2018
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 60 citations in OpenAlex.
- CircACVR2A(2-4) regulates stem cell pluripotency by uncoupling CDK-activating kinase functions.Nucleic acids research · 2026Article
- A highly abundant circular RNA from the RMST locus plays a role in posterior fossa ependymoma pathogenesis.Brain pathology (Zurich, Switzerland) · 2026Article
- lncRNAs: a new generation of targets and biomarkers in thyroid cancer.European thyroid journal · 2026Review
- CircTarget: a comprehensive database of circRNA-target RNA interactions across multiple cell types.Nucleic acids research · 2026Article
- Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation.Cancer cell · 2025Article
- Article
- Circular RNAs in Archaea.Advances in experimental medicine and biology · 2025Review
- Circ_0003764 Regulates the Osteogenic Differentiation of Periodontal Ligament Stem Cells.International dental journal · 2024Article
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Early-stage idiopathic Parkinson's disease is associated with reduced circular RNA expression.NPJ Parkinson's disease · 2024Article
- A systematic analysis of circRNAs in subnuclear compartments.RNA biology · 2024Article
- CAG repeat expansion in the Huntington's disease gene shapes linear and circular RNAs biogenesis.PLoS genetics · 2023Article
- Emerging roles of circular RNAs in stem cells.Genes & diseases · 2023Review
- Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.Nature methods · 2023Article
- A Circular RNA Expressed from the FAT3 Locus Regulates Neural Development.Molecular neurobiology · 2023Article
- Retinitis pigmentosa-associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells.Life science alliance · 2023Article
- Circular RNAs: New players involved in the regulation of cognition and cognitive diseases.Frontiers in neuroscience · 2023Review
- Noncoding RNAs: Novel Targets for Opioid Tolerance.Current neuropharmacology · 2023Review
- Circular RNA circFIRRE drives osteosarcoma progression and metastasis through tumorigenic-angiogenic coupling.Molecular cancer · 2022Article
- Significant reduction of long non-coding RNAs expression in bipolar disorder.BMC psychiatry · 2022Article
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundCircular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina.
resultsA transcriptome-wide increase in circRNA expression, size, and exon count was observed, with circRNA levels reaching a plateau by day 45. Parallel statistical analyses, controlling for sample and locus specific effects, identified 239 circRNAs with expression changes distinct from the transcriptome-wide pattern, but these all also increased in abundance over time. Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes. The most abundant, circRMST:E12-E6, showed a > 100X increase during differentiation accompanied by an isoform switch, and accounts for > 99% of RMST transcripts in many adult tissues. The second most abundant, circFIRRE:E10-E5, accounts for > 98% of FIRRE transcripts in differentiating human ES cells, and is one of 39 FIRRE circRNAs, many of which include multiple unannotated exons.
conclusionsOur results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled. They also suggest that RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, are processed as circular lncRNAs with only minor linear species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.