ArticleCell systems2019
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 86 citations in OpenAlex.
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- Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes.Nature communications · 2025Article
- Three-dimensional regulatory hubs support oncogenic programs in glioblastoma.Molecular cell · 2025Article
- Element-specific estimation of background mutation rates in whole cancer genomes through transfer learning.NPJ precision oncology · 2025Article
- Three-dimensional regulatory hubs support oncogenic programs in glioblastoma.bioRxiv : the preprint server for biology · 2024Article
- MLSNet: a deep learning model for predicting transcription factor binding sites.Briefings in bioinformatics · 2024Article
- Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.Nucleic acids research · 2024Article
- Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation.Molecular cell · 2024Article
- Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors.Molecular cancer · 2023Article
- Landscape of enhancer disruption and functional screen in melanoma cells.Genome biology · 2023Article
- Recapitulation of patient-specific 3D chromatin conformation using machine learning.Cell reports methods · 2023Article
- Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial.Nature communications · 2023Article
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.Scientific reports · 2023Article
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 2023Article
- Tumour mutations in long noncoding RNAs enhance cell fitness.Nature communications · 2023Article
- Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.bioRxiv : the preprint server for biology · 2023Article
- Alterations of cohesin complex genes in acute myeloid leukemia: differential co-mutations, clinical presentation and impact on outcome.Blood cancer journal · 2023Article
- maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.PLoS computational biology · 2023Article
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Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
Abstract
Recent studies have shown that mutations at non-coding elements, such as promoters and enhancers, can act as cancer drivers. However, an important class of non-coding elements, namely CTCF insulators, has been overlooked in the previous driver analyses. We used insulator annotations from CTCF and cohesin ChIA-PET and analyzed somatic mutations in 1,962 whole genomes from 21 cancer types. Using the heterogeneous patterns of transcription-factor-motif disruption, functional impact, and recurrence of mutations, we developed a computational method that revealed 21 insulators showing signals of positive selection. In particular, mutations in an insulator in multiple cancer types, including 16% of melanoma samples, are associated with TGFB1 up-regulation. Using CRISPR-Cas9, we find that alterations at two of the most frequently mutated regions in this insulator increase cell growth by 40%-50%, supporting the role of this boundary element as a cancer driver. Thus, our study reveals several CTCF insulators as putative cancer drivers.
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