ArticleBMC genomics2015
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- The Goldilocks state of transcriptional readthrough for chimeric splicing.Transcription · 2026Review
- Regulatory Mechanisms and Functional Roles of Readthrough Transcripts in Tumorigenesis.International journal of molecular sciences · 2025Review
- Comprehensive resource for transcription readthrough events in healthy human tissues.Scientific data · 2025Article
- [Read-through circular RNA rt-circ-HS promotes hypoxia inducible factor 1α expression and renal carcinoma cell proliferation, migration and invasiveness].Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences · 2023Article
- Pattern recognition in the landscape of seemingly random chimeric transcripts.Computational and structural biotechnology journal · 2023Article
- Seven key hub genes identified by gene co-expression network in cutaneous squamous cell carcinoma.BMC cancer · 2021Article
- A HIF1α-GPD1 feedforward loop inhibits the progression of renal clear cell carcinoma via mitochondrial function and lipid metabolism.Journal of experimental & clinical cancer research : CR · 2021Article
- Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer.International journal of molecular sciences · 2019Review
- Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer.Neoplasia (New York, N.Y.) · 2019Article
- A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes.Nucleic acids research · 2019Article
- Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma.Oncotarget · 2018Article
- ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.BMC genomics · 2017Article
- Read-through transcripts in normal human lung parenchyma are down-regulated in lung adenocarcinoma.Oncotarget · 2016Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChimeric read-through RNAs are transcripts originating from two directly adjacent genes (<10 kb) on the same DNA strand. Although they are found in next-generation whole transcriptome sequencing (RNA-Seq) data on a regular basis, investigating them further has usually been refrained from. Therefore, their expression patterns or functions in general, and in oncogenesis in particular, are poorly understood.
resultsWe used paired-end RNA-Seq and a specifically designed computational data analysis pipeline (FusionSeq) to nominate read-through events in a small discovery set of renal cell carcinomas (RCC) and confirmed them in a larger validation cohort. 324 read-through events were called overall; 22/27 (81%) selected nominees passed validation with conventional PCR and were sequenced at the junction region. We frequently identified various isoforms of a given read-through event. 2/22 read-throughs were up-regulated: BC039389-GATM was higher expressed in RCC compared to benign adjacent kidney; KLK4-KRSP1 was expressed in 46/169 (27%) RCCs, but rarely in normal tissue. KLK4-KRSP1 expression was associated with worse clinical outcome in the patient cohort. In cell lines, both read-throughs influenced molecular mechanisms (i.e. target gene expression or migration/invasion) in a way that counteracted the effect of the respective parent transcript GATM or KLK4.
conclusionsOur data suggests that the up-regulation of read-through RNA chimeras in tumors is not random but causes regulatory effects on cellular mechanisms and may impact patient survival.
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