ArticleGenome biology2009
Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 69 citations in OpenAlex.
- Functional Characterization of Long Non-Coding RNAs Associated with Reproductive Fitness in Pura Raza Española Mares.Animals : an open access journal from MDPI · 2026Article
- Article
- FOXA3 regulates cholesterol metabolism to compensate for low uptake during the progression of lung adenocarcinoma.PLoS biology · 2024Article
- PRKAG2.2 is essential for FoxA1Science advances · 2023Article
- The role of FOXA family transcription factors in glucolipid metabolism and NAFLD.Frontiers in endocrinology · 2023Review
- Coronatine Enhances Chilling Tolerance of Tomato Plants by Inducing Chilling-Related Epigenetic Adaptations and Transcriptional Reprogramming.International journal of molecular sciences · 2022Article
- PGC1α Cooperates with FOXA1 to Regulate Epithelial Mesenchymal Transition through the TCF4-TWIST1.International journal of molecular sciences · 2022Article
- Different subpopulations of regulatory T cells in human autoimmune disease, transplantation, and tumor immunity.MedComm · 2022Review
- The pioneer and differentiation factor FOXA2 is a key driver of yolk-sac tumour formation and a new biomarker for paediatric and adult yolk-sac tumours.Journal of cellular and molecular medicine · 2021Article
- Suppression of Cell Tumorigenicity by Non-neural Pro-differentiation Factors via Inhibition of Neural Property in Tumorigenic Cells.Frontiers in cell and developmental biology · 2021Article
- Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells.Chemical research in toxicology · 2020Article
- Hepatic Forkhead Box Protein A3 Regulates ApoA-I (Apolipoprotein A-I) Expression, Cholesterol Efflux, and Atherogenesis.Arteriosclerosis, thrombosis, and vascular biology · 2019Article
- FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes.Nature · 2019Article
- Accurate prediction of cell type-specific transcription factor binding.Genome biology · 2019Article
- Temporal regulation of epithelium formation mediated by FoxA, MKLP1, MgcRacGAP, and PAR-6.Molecular biology of the cell · 2017Article
- PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.Nucleic acids research · 2017Article
- FOXN3 Regulates Hepatic Glucose Utilization.Cell reports · 2016Article
- Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.Human genetics · 2016Article
- Pioneer transcription factors, chromatin dynamics, and cell fate control.Current opinion in genetics & development · 2016Review
- Modeling co-occupancy of transcription factors using chromatin features.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes.
resultsHere, we present a genome-wide location analysis of FOXA1 and FOXA3 binding sites in HepG2 cells through chromatin immunoprecipitation with detection by sequencing (ChIP-seq) studies and compare these with our previous results on FOXA2. We found that these factors often bind close to each other in different combinations and consecutive immunoprecipitation of chromatin for one and then a second factor (ChIP-reChIP) shows that this occurs in the same cell and on the same DNA molecule, suggestive of molecular interactions. Using co-immunoprecipitation, we further show that FOXA2 interacts with both FOXA1 and FOXA3 in vivo, while FOXA1 and FOXA3 do not appear to interact. Additionally, we detected diverse patterns of trimethylation of lysine 4 on histone H3 (H3K4me3) at transcriptional start sites and directionality of this modification at FOXA binding sites. Using the sequence reads at polymorphic positions, we were able to predict allele specific binding for FOXA1, FOXA3, and H3K4me3. Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions.
conclusionsWe find that ChIP-seq can be used not only to create gene regulatory maps but also to predict molecular interactions and to inform on the mechanisms for common quantitative variation.
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