ArticleBMC genomics2013
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer.Artificial intelligence in medicine · 2025Article
- DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.Genomics, proteomics & bioinformatics · 2024Article
- abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.BMC bioinformatics · 2022Article
- Measuring significant changes in chromatin conformation with ACCOST.Nucleic acids research · 2020Article
- HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data.Computational and structural biotechnology journal · 2020Article
- IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.Computational and structural biotechnology journal · 2020Article
- Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51.Cell reports · 2019Article
- Selfish: discovery of differential chromatin interactions via a self-similarity measure.Bioinformatics (Oxford, England) · 2019Article
- Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance.Nature communications · 2019Article
- Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature.Journal of cellular biochemistry · 2019Article
- BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.Frontiers in genetics · 2019Article
- Article
- Reprimo, a Potential p53-Dependent Tumor Suppressor Gene, Is Frequently Hypermethylated in Estrogen Receptor α-Positive Breast Cancer.International journal of molecular sciences · 2017Article
- Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma.Scientific reports · 2017Article
- Long-range control of gene expression via RNA-directed DNA methylation.PLoS genetics · 2017Article
- HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.Genome biology · 2016Article
- Chromosomal Translocations in Black Flies (Diptera: Simuliidae)-Facilitators of Adaptive Radiation?PloS one · 2016Article
- Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.Genome biology · 2015Article
- Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundAn emerging Hi-C protocol has the ability to probe three-dimensional (3D) architecture and capture chromatin interactions in a genome-wide scale. It provides informative results to address how chromatin organization changes contribute to disease/tumor occurrence and progression in response to stimulation of environmental chemicals or hormones.
resultsIn this study, using MCF7 cells as a model system, we found estrogen stimulation significantly impact chromatin interactions, leading to alteration of gene regulation and the associated histone modification states. Many chromosomal interaction regions at different levels of interaction frequency were identified. In particular, the top 10 hot regions with the highest interaction frequency are enriched with breast cancer specific genes. Furthermore, four types of E2-mediated strong differential (gain- or loss-) chromosomal (intra- or inter-) interactions were classified, in which the number of gain-chromosomal interactions is less than the number of loss-chromosomal interactions upon E2 stimulation. Finally, by integrating with eight histone modification marks, DNA methylation, regulatory elements regions, ERα and Pol-II binding activities, associations between epigenetic patterns and high chromosomal interaction frequency were revealed in E2-mediated gene regulation.
conclusionsThe work provides insight into the effect of chromatin interaction on E2/ERα regulated downstream genes in breast cancer cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.