ArticleComputational and structural biotechnology journal2021
The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers.
Article in Computational and structural biotechnology journal, 2021. 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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15 citing papers in PubMed, 17 citations in OpenAlex.
- 3D chromatin architecture in cancer: mechanisms of dysregulation and emerging therapeutic strategies.Experimental & molecular medicine · 2026Review
- The hierarchical folding dynamics of topologically associating domains during early embryo development.BMC biology · 2025Article
- 3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression.Communications biology · 2025Article
- THz Waves Improve Spatial Working Memory by Increasing the Activity of Glutamatergic Neurons in Mice.Cells · 2025Article
- Polyphenols bind G4-Quadruplex structures and act as epigenetic modifiers with anti-cancer effects.EXCLI journal · 2025Review
- Beyond the Synapse:International journal of molecular sciences · 2024Review
- HTAD: a human-in-the-loop framework for supervised chromatin domain detection.Genome biology · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.Briefings in bioinformatics · 2024Article
- 3D genomic organization in cancers.Quantitative biology (Beijing, China) · 2023Review
- Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.Journal of animal science and biotechnology · 2023Article
- MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.Nature communications · 2022Article
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.Communications biology · 2022Article
- Multilevel view on chromatin architecture alterations in cancer.Frontiers in genetics · 2022Review
- PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.Computational and structural biotechnology journal · 2021Article
Corrections and comments
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Authors and funding
23 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a "TAD hierarchical score (TH score)" for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.
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