ArticleBioinformatics (Oxford, England)2012
Novel domain combinations in proteins encoded by chimeric transcripts.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Uncovering the domain language of protein functionality and cell phenotypes using DANSy.bioRxiv : the preprint server for biology · 2025Article
- The role of genome composition and activation in shaping the translocation landscape in health and disease.Medical research archives · 2025Article
- p160 nuclear receptor coactivator family members and their role in rare fusion‑driven neoplasms (Review).Oncology letters · 2024Review
- Article
- EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains.FEBS open bio · 2021Article
- Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis.Journal of visualized experiments : JoVE · 2020Article
- ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.Nucleic acids research · 2020Article
- Molecular Signatures of Fusion Proteins in Cancer.ACS pharmacology & translational science · 2019Article
- Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer.Scientific reports · 2019Article
- Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.Briefings in bioinformatics · 2018Article
- Review
- ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.Nucleic acids research · 2017Article
- ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.Nucleic acids research · 2017Article
- Discovering and understanding oncogenic gene fusions through data intensive computational approaches.Nucleic acids research · 2016Review
- Read-through transcripts in normal human lung parenchyma are down-regulated in lung adenocarcinoma.Oncotarget · 2016Article
- Evolutionary Insights into RNA trans-Splicing in Vertebrates.Genome biology and evolution · 2016Review
- NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.Nucleic acids research · 2016Article
- ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.Nucleic acids research · 2015Article
- Article
- Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?Nucleic acids research · 2014Article
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2 authors.
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Abstract
motivationChimeric RNA transcripts are generated by different mechanisms including pre-mRNA trans-splicing, chromosomal translocations and/or gene fusions. It was shown recently that at least some of chimeric transcripts can be translated into functional chimeric proteins.
resultsTo gain a better understanding of the design principles underlying chimeric proteins, we have analyzed 7,424 chimeric RNAs from humans. We focused on the specific domains present in these proteins, comparing their permutations with those of known human proteins. Our method uses genomic alignments of the chimeras, identification of the gene-gene junction sites and prediction of the protein domains. We found that chimeras contain complete protein domains significantly more often than in random data sets. Specifically, we show that eight different types of domains are over-represented among all chimeras as well as in those chimeras confirmed by RNA-seq experiments. Moreover, we discovered that some chimeras potentially encode proteins with novel and unique domain combinations. Given the observed prevalence of entire protein domains in chimeras, we predict that certain putative chimeras that lack activation domains may actively compete with their parental proteins, thereby exerting dominant negative effects. More generally, the production of chimeric transcripts enables a combinatorial increase in the number of protein products available, which may disturb the function of parental genes and influence their protein-protein interaction network. AVAILABILITY: our scripts are available upon request.
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