ArticlePLoS computational biology2019
Aberrant DNA methylation defines isoform usage in cancer, with functional implications.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- The identification of RNA splicing aberrations and their potential regulatory network in Chinese non-small cell lung cancer.Respiratory research · 2026Article
- Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications.Current oncology (Toronto, Ont.) · 2024Review
- Time series-based hybrid ensemble learning model with multivariate multidimensional feature coding for DNA methylation prediction.BMC genomics · 2023Article
- Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.PLoS computational biology · 2023Article
- Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome.Epigenetics · 2022Article
- Characterization and clustering of kinase isoform expression in metastatic melanoma.PLoS computational biology · 2022Article
- Genome-Wide Analysis for the Regulation of Gene Alternative Splicing by DNA Methylation Level in Glioma and its Prognostic Implications.Frontiers in genetics · 2022Article
- The role of TGR5 as an onco-immunological biomarker in tumor staging and prognosis by encompassing the tumor microenvironment.Frontiers in oncology · 2022Article
- A history of childhood maltreatment is associated with altered DNA methylation levels of DNA methyltransferase 1 in maternal but not neonatal mononuclear immune cells.Frontiers in psychiatry · 2022Article
- Epigenetic interplay between methylation and miRNA in bladder cancer: focus on isoform expression.BMC genomics · 2021Article
- Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer.Scientific reports · 2021Article
- Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs.Biomedicines · 2021Article
- Article
- Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines.Thyroid : official journal of the American Thyroid Association · 2020Article
- DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex.Molecular cell · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Alternative transcript isoforms are common in tumors and act as potential drivers of cancer. Mechanisms determining altered isoform expression include somatic mutations in splice regulatory sites or altered splicing factors. However, since DNA methylation is known to regulate transcriptional isoform activity in normal cells, we predicted the highly dysregulated patterns of DNA methylation present in cancer also affect isoform activity. We analyzed DNA methylation and RNA-seq isoform data from 18 human cancer types and found frequent correlations specifically within 11 cancer types. Examining the top 25% of variable methylation sites revealed that the location of the methylated CpG site in a gene determined which isoform was used. In addition, the correlated methylation-isoform patterns classified tumors into known subtypes and predicted distinct protein functions between tumor subtypes. Finally, methylation-correlated isoforms were enriched for oncogenes, tumor suppressors, and cancer-related pathways. These findings provide new insights into the functional impact of dysregulated DNA methylation in cancer and highlight the relationship between the epigenome and transcriptome.
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