ArticleJournal of molecular evolution2009
Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes.
Article in Journal of molecular evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 88 citations in OpenAlex.
- Crosstalk Between R-Loops, RNA/DNA Modifications, and Cell Death Dynamics in Canine Models of Retinitis Pigmentosa.Investigative ophthalmology & visual science · 2026Article
- Chimeric RNA isoforms generated by diverse mechanisms from two C-type lectins modulate innate immunity in arthropods.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea.Frontiers in plant science · 2025Article
- Conserved features and diversity attributes of chimeric RNAs across accessions in four plants.Plant biotechnology journal · 2024Article
- Identification of circular RNAs hosted by theRNA biology · 2023Article
- Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer.International journal of molecular sciences · 2022Review
- Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts.Nature communications · 2021Article
- Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy.Cancer letters · 2021Review
- SARS-CoV-2-Host Chimeric RNA-Sequencing Reads Do Not Necessarily Arise From Virus Integration Into the Host DNA.Frontiers in microbiology · 2021Article
- The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer.Journal of genetics and genomics = Yi chuan xue bao · 2020Article
- Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts.Molecular therapy. Nucleic acids · 2020Article
- Interior circular RNA.RNA biology · 2020Article
- A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens.Frontiers in immunology · 2020Review
- Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer.International journal of molecular sciences · 2019Review
- LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells.Epigenomes · 2019Review
- A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes.Nucleic acids research · 2019Article
- Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.Briefings in bioinformatics · 2018Article
- Chimeric RNA in Cancer and Stem Cell Differentiation.Stem cells international · 2018Review
- It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research.International journal of molecular sciences · 2017Review
- ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chimeric RNAs have been reported in varieties of organisms and are conventionally thought to be produced by trans-splicing of two or more distinct transcripts. Here, we conducted a large-scale search for chimeric RNAs in the budding yeast, fruit fly, mouse, and human. Thousands of chimeric transcripts were identified in these organisms except in yeast, in which five chimeric RNAs were observed. RT-PCR experiments for a sample of yeast and fly chimeric transcripts using specific primers show that about one-third of these chimeric RNAs can be reproduced. The results suggest that at least a considerable amount of chimeric RNAs is unlikely from aberrant transcription or splicing, and thus formation of chimeric RNAs is probably a widespread process and can greatly contribute to the complexity of the transcriptome and proteome of organisms. However, only a small fraction (<20%) of these chimeric RNAs has GU-AG at the junction sequences which fits the classical trans-splicing model. In contrast, we observed that about half of the chimeric RNAs have short homologous sequences (SHSs) at the junction sites of the source sequences. Our sequence mutation experiments in yeast showed that disruption of SHSs resulted in the disappearance of the corresponding chimeric RNAs, suggesting that SHSs are essential for generating this kind of chimeric RNA. In addition to the classical trans-splicing model, we propose a new model, the transcriptional slippage model, to explain the generation of those chimeric RNAs synthesized from templates with SHSs.
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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.