ArticleNucleic acids research2018
Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Diagnostic and prognostic role of circular RNAs: Analytical challenges and emerging opportunities.iScience · 2026Review
- Comparative genomics reveals LINE-1 recombination with diverse RNAs.Cell genomics · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Development of Mathematical Models Using circRNA Combinations (International journal of molecular sciences · 2025Article
- Transcriptome-scale analysis of functional alternative back-splicing events in colorectal cancer.Journal of translational medicine · 2025Article
- Exploring the Post Mortem Interval (PMI) Estimation Model by circRNAInternational journal of molecular sciences · 2025Article
- Fusion Challenges in Solid Tumors: Shaping the Landscape of Cancer Care in Precision Medicine.JCO precision oncology · 2024Review
- Characterization ofNAR genomics and bioinformatics · 2024Article
- Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus.The plant genome · 2024Article
- FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing.Nucleic acids research · 2024Article
- Article
- mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy.Nature communications · 2023Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- Drug screening at single-organoid resolution via bioprinting and interferometry.Nature communications · 2023Article
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
- Circular RNA and intervertebral disc degeneration: unravelling mechanisms and implications.Frontiers in molecular biosciences · 2023Review
- Identification and characterization of circular RNA in the model of autism spectrum disorder from PMFrontiers in genetics · 2023Article
- Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism.Molecular psychiatry · 2022Article
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of poly(A)- and non-poly(A)-selected RNA-seq data from diverse human cell lines to distinguish between tsRNAs and circRNAs. We identified 24,498 NCL events and found that a considerable proportion (20-35%) of them arise from both tsRNAs and circRNAs, representing extensive alternative trans-splicing and cis-backsplicing in human cells. We show that sequence generalities of exon circularization are also observed in tsRNAs. Recapitulation of NCL RNAs further shows that inverted Alu repeats can simultaneously promote the formation of tsRNAs and circRNAs. However, tsRNAs and circRNAs exhibit quite different, or even opposite, expression patterns, in terms of correlation with the expression of their co-linear counterparts, expression breadth/abundance, transcript stability, and subcellular localization preference. These results indicate that tsRNAs and circRNAs may play different regulatory roles and analysis of NCL events should take the joint effects of different NCL-splicing types and joint effects of multiple NCL events into consideration. This study describes the first transcriptome-wide analysis of trans-splicing and cis-backsplicing, expanding our understanding of the complexity of the human transcriptome.
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