ArticleProceedings of the National Academy of Sciences of the United States of America2007
Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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69 citing papers in PubMed, 112 citations in OpenAlex.
- Functional chromatin signatures premark future lineage-specific enhancers.Cell genomics · 2026Article
- Epigenetic pioneering by SWI/SNF family remodelers.Molecular cell · 2024Review
- Cell-free DNA methylation patterns in aging and their association with inflamm-aging.Epigenomics · 2024Article
- 1α,25(OH)Journal for immunotherapy of cancer · 2022Article
- Loss of Monoallelic Expression ofFrontiers in genetics · 2022Article
- Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.The Journal of experimental medicine · 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
- Primed histone demethylation regulates shoot regenerative competency.Nature communications · 2019Article
- Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus.PLoS genetics · 2019Article
- From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo.Developmental cell · 2018Article
- Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes.Cellular and molecular life sciences : CMLS · 2018Review
- Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes.International journal of molecular sciences · 2018Article
- Methods for discovering genomic loci exhibiting complex patterns of differential methylation.BMC bioinformatics · 2017Article
- Hepatic deficiency of the pioneer transcription factor FoxA restricts hepatitis B virus biosynthesis by the developmental regulation of viral DNA methylation.PLoS pathogens · 2017Article
- Regulating role of fetal thyroid hormones on placental mitochondrial DNA methylation: epidemiological evidence from the ENVIRClinical epigenetics · 2017Article
- PBX1 as Pioneer Factor: A Case Still Open.Frontiers in cell and developmental biology · 2017Review
- Genetic and Epigenetic Regulation of PD-1 Expression.Journal of immunology (Baltimore, Md. : 1950) · 2016Review
- Epigenetic regulation of the expression of Il12 and Il23 and autoimmune inflammation by the deubiquitinase Trabid.Nature immunology · 2016Article
- FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity.Cell stem cell · 2016Article
- Brain-specific epigenetic markers of schizophrenia.Translational psychiatry · 2015Article
9 more citing papers are in PubMed but not listed here.
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9 authors at 4 institutions in 1 country.
Funding
Abstract
Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.
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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.