ArticleGenome research2014
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Multiple intron motifs have redundant functions in the trans-splicing of the mod(mdg4) locus.Nucleic acids research · 2026Article
- lncRNAs: a new generation of targets and biomarkers in thyroid cancer.European thyroid journal · 2026Review
- Therapeutic targeting of RNA for neurological and neuromuscular disease.Genes & development · 2024Review
- Characterization ofNAR genomics and bioinformatics · 2024Article
- mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy.Nature communications · 2023Article
- CTNNBIP1-CLSTN1 functions as a housekeeping chimeric RNA and regulates cell proliferation through SERPINE2.Cell death discovery · 2023Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- CTNNBIP1-CLSTN1 Functions as a Housekeeping Chimeric RNA, and Regulates Cell Proliferation through SERPINE2.Research square · 2023Article
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
- Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology.Nature communications · 2023Article
- Article
- LncRNAs and their RBPs: How to influence the fate of stem cells?Stem cell research & therapy · 2022Review
- Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer.International journal of molecular sciences · 2022Review
- Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing.RNA biology · 2021Article
- Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells.NAR genomics and bioinformatics · 2021Article
- RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets.Trends in pharmacological sciences · 2021Review
- Article
- The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease.International journal of molecular sciences · 2021Review
- Fusion Genes and RNAs in Cancer Development.Non-coding RNA · 2021Review
- Long Non-coding RNA Rhabdomyosarcoma 2-Associated Transcript Regulates Angiogenesis in Endothelial Cells.Frontiers in physiology · 2021Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Trans-splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans-splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platform-dependent experimental artifacts of RNA sequencing. We successfully identified and confirmed four trans-spliced RNAs, including the first reported trans-spliced large intergenic noncoding RNA ("tsRMST"). We showed that these trans-spliced RNAs were all highly expressed in human pluripotent stem cells and differentially expressed during hESC differentiation. Our results further indicated that tsRMST can contribute to pluripotency maintenance of hESCs by suppressing lineage-specific gene expression through the recruitment of NANOG and the PRC2 complex factor, SUZ12. Taken together, our findings provide important insights into the role of trans-splicing in pluripotency maintenance of hESCs and help to facilitate future studies into trans-splicing, opening up this important but understudied class of post-transcriptional events for comprehensive characterization.
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