ArticleBMC genomics2014
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 47 citations in OpenAlex.
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- Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C.Epigenetics & chromatin · 2022Article
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- BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation.Science advances · 2021Article
- TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development.Cellular and molecular life sciences : CMLS · 2020Review
- TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.PLoS genetics · 2020Article
- BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene.British journal of cancer · 2020Article
- Gene-Specific Actions of Transcriptional Coregulators Facilitate Physiological Plasticity: Evidence for a Physiological Coregulator Code.Trends in biochemical sciences · 2020Review
- Chromatin interactome mapping at 139 independent breast cancer risk signals.Genome biology · 2020Article
- CSA: a web service for the complete process of ChIP-Seq analysis.BMC bioinformatics · 2019Article
- MCF-7 as a Model for Functional Analysis of Breast Cancer Risk Variants.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2019Article
- A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome.Nature communications · 2019Article
- Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Science advances · 2018Article
- Beyond DNA: the Role of Epigenetics in the Premalignant Progression of Breast Cancer.Journal of mammary gland biology and neoplasia · 2018Review
- Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe precise nature of how cell type specific chromatin structures at enhancer sites affect gene expression is largely unknown. Here we identified cell type specific enhancers coupled with gene expression in two different types of breast epithelial cells, HMEC (normal breast epithelial cells) and MDAMB231 (triple negative breast cancer cell line).
resultsEnhancers were defined by modified neighboring histones [using chromatin immunoprecipitation followed by sequencing (ChIP-seq)] and nucleosome depletion [using formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq)]. Histone modifications at enhancers were related to the expression levels of nearby genes up to 750 kb away. These expression levels were correlated with enhancer status (poised or active), defined by surrounding histone marks. Furthermore, about fifty percent of poised and active enhancers contained nucleosome-depleted regions. We also identified response element motifs enriched at these enhancer sites that revealed key transcription factors (e.g. TP63) likely involved in regulating breast epithelial enhancer-mediated gene expression. By utilizing expression data, potential target genes of more than 600 active enhancers were identified. These genes were involved in proteolysis, epidermis development, cell adhesion, mitosis, cell cycle, and DNA replication.
conclusionsThese findings facilitate the understanding of epigenetic regulation specifically, such as the relationships between regulatory elements and gene expression and generally, how breast epithelial cellular phenotypes are determined by cell type specific enhancers.
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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.