ArticleBMC medical genomics2014
The global landscape of intron retentions in lung adenocarcinoma.
Article in BMC medical genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- DecodingbioRxiv : the preprint server for biology · 2025Article
- Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing.Life science alliance · 2024Article
- Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia.Molecular therapy. Nucleic acids · 2024Article
- Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads.Genome biology · 2022Article
- Differential fates of introns in gene expression due to global alternative splicing.Human genetics · 2022Review
- iREAD: a tool for intron retention detection from RNA-seq data.BMC genomics · 2020Article
- Intron Retention as a Mode for RNA-Seq Data Analysis.Frontiers in genetics · 2020Review
- Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients.International journal of molecular sciences · 2019Article
- Intron retention enhances gene regulatory complexity in vertebrates.Genome biology · 2017Article
- Environmental perturbations lead to extensive directional shifts in RNA processing.PLoS genetics · 2017Article
- The bromodomain protein BRD4 regulates splicing during heat shock.Nucleic acids research · 2017Article
- The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing.PLoS pathogens · 2016Article
- Phospholipid profiling identifies acyl chain elongation as a ubiquitous trait and potential target for the treatment of lung squamous cell carcinoma.Oncotarget · 2016Article
- Dysregulation of splicing proteins in head and neck squamous cell carcinoma.Cancer biology & therapy · 2016Article
- Non-small cell lung cancer is characterized by dramatic changes in phospholipid profiles.International journal of cancer · 2015Article
- Targeting the spliceosome in chronic lymphocytic leukemia with the macrolides FD-895 and pladienolide-B.Haematologica · 2015Article
- Tissue- and case-specific retention of intron 40 in mature dystrophin mRNA.Journal of human genetics · 2015Article
- Alternative splicing acting as a bridge in evolution.Stem cell investigation · 2015Article
- Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs.Evolutionary bioinformatics online · 2014Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe transcriptome complexity in an organism can be achieved by alternative splicing of precursor messenger RNAs. It has been revealed that alternations in mRNA splicing play an important role in a number of diseases including human cancers.
methodsIn this study, we exploited whole transcriptome sequencing data from five lung adenocarcinoma tissues and their matched normal tissues to interrogate intron retention, a less studied alternative splicing form which has profound structural and functional consequence by modifying open reading frame or inserting premature stop codons.
resultsAbundant intron retention events were found in both tumor and normal tissues, and 2,340 and 1,422 genes only contain tumor-specific retentions and normal-specific retentions, respectively. Combined with gene expression analysis, we showed that genes with tumor-specific retentions tend to be over-expressed in tumors, and the abundance of intron retention within genes is negatively related with gene expression, indicating the action of nonsense mediated decay. Further functional analysis demonstrated that genes with tumor-specific retentions include known lung cancer driver genes and are found enriched in pathways important in carcinogenesis.
conclusionsWe hypothesize that intron retentions and consequent nonsense mediated decay may collectively counteract the over-expression of genes promoting cancer development. Identification of genes with tumor-specific retentions may also help develop targeted therapies.
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