ArticleGenome research2010
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.
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Who cites it
82 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules.BMC genomics · 2013Pooled it
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- Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response.Communications biology · 2024Article
- HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements.Communications biology · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators.Cell genomics · 2023Article
- Differential CpG methylation atbioRxiv : the preprint server for biology · 2023Article
- XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.Science advances · 2023Article
- YY1 Regulates Glucose Homeostasis Through Controlling Insulin Transcription in Pancreatic β-Cells.Diabetes · 2022Article
- Genome-wide analysis of the XTH gene family and functional analysis ofFrontiers in plant science · 2022Article
- Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss.BMC genomics · 2021Article
- Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues.Frontiers in genetics · 2021Article
- Transcription factor GLIS3: Critical roles in thyroid hormone biosynthesis, hypothyroidism, pancreatic beta cells and diabetes.Pharmacology & therapeutics · 2020Review
- Review
- H3K4me1 Distribution Predicts Transcription State and Poising at Promoters.Frontiers in cell and developmental biology · 2020Article
- Identification ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Hepatocyte Nuclear Factor 4 Alpha Activation Is Essential for Termination of Liver Regeneration in Mice.Hepatology (Baltimore, Md.) · 2019Article
- Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification.Nature communications · 2019Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
The liver and pancreas share a common origin and coexpress several transcription factors. To gain insight into the transcriptional networks regulating the function of these tissues, we globally identify binding sites for FOXA2 in adult mouse islets and liver, PDX1 in islets, and HNF4A in liver. Because most eukaryotic transcription factors bind thousands of loci, many of which are thought to be inactive, methods that can discriminate functionally active binding events are essential for the interpretation of genome-wide transcription factor binding data. To develop such a method, we also generated genome-wide H3K4me1 and H3K4me3 localization data in these tissues. By analyzing our binding and histone methylation data in combination with comprehensive gene expression data, we show that H3K4me1 enrichment profiles discriminate transcription factor occupied loci into three classes: those that are functionally active, those that are poised for activation, and those that reflect pioneer-like transcription factor activity. Furthermore, we demonstrate that the regulated presence of H3K4me1-marked nucleosomes at transcription factor occupied promoters and enhancers controls their activity, implicating both tissue-specific transcription factor binding and nucleosome remodeling complex recruitment in determining tissue-specific gene expression. Finally, we apply these approaches to generate novel insights into how FOXA2, PDX1, and HNF4A cooperate to drive islet- and liver-specific gene expression.
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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.