ArticleMolecular oncology2022
Computational characterization of domain-segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis.
Article in Molecular oncology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Hierarchical Prediction and Perturbation of Chromatin Organization Reveal How Loop Domains Mediate Higher-Order Architectures.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Extensive epigenomic dysregulation is a hallmark of homologous recombination deficiency in triple-negative breast cancer.International journal of cancer · 2025Article
- The Diversity of Methylation Patterns in Serous Borderline Ovarian Tumors and Serous Ovarian Carcinomas.Cancers · 2024Article
- Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer.Molecular cancer · 2024Article
- Carcinoma of unknown primary (CUP): an update for histopathologists.Cancer metastasis reviews · 2023Review
- A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health.BMC medicine · 2023Article
- Targeted DNA Demethylation: Vectors, Effectors and Perspectives.Biomedicines · 2023Review
- Characterization of network hierarchy reflects cell state specificity in genome organization.Genome research · 2023Article
- Expression regulation of genes is linked to their CpG density distributions around transcription start sites.Life science alliance · 2022Article
- Pseudogenes and Liquid Phase Separation in Epigenetic Expression.Frontiers in oncology · 2022Review
- Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high-order chromatin structure, together with DNA methylation and other epigenetic marks, plays a vital role in gene regulation and displays abnormal status in cancer cells. Theoretical analyses are expected to provide a more unified understanding of the multi-omics data on the large variety of samples, and hopefully a common picture of carcinogenesis. In particular, we are interested in the question of whether an underlying origin DNA sequence exists for these epigenetic alterations. The human genome consists of two types of megabase-sized domain based on the distribution of CpG islands (CGIs) that show distinct structural, epigenetic, and transcriptional properties: CGI-rich and CGI-poor domains. Through an integrated analysis of chromatin structure, DNA methylation, and RNA sequencing data, we found that, in carcinogenesis, the two different types of domain display different structural changes and have an increased number of DNA methylation differences and transcriptional-level differences, compared with in noncancer cells. We also compared the structural features among carcinogenesis, senescence, and mitosis, showing the possible connection between chromatin structure and cell state, which could affect vital cancer-related properties. In summary, chromatin structure, DNA methylation, and gene expression, as well as their changes observed in several types of cancers, show a dependence on multiscale DNA sequence heterogeneity.
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Registered trials
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