ArticleEpigenetics & chromatin2016
Chromatin variation associated with liver metabolism is mediated by transposable elements.
Article in Epigenetics & chromatin, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 36 citations in OpenAlex.
- Intermittent fasting rewires tissue-specific gene-transposable element regulatory networks.PNAS nexus · 2026Article
- Extrachromosomal Circular DNA and Transposable Elements in Type 2 Diabetes.International journal of molecular sciences · 2025Review
- Reactivation of retrotransposable elements is associated with environmental stress and ageing.Nature reviews. Genetics · 2025Review
- Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse.Mobile DNA · 2024Article
- Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.Frontiers in genetics · 2024Article
- Review
- Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors.Development (Cambridge, England) · 2022Article
- Roles of transposable elements in the regulation of mammalian transcription.Nature reviews. Molecular cell biology · 2022Review
- A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function.eLife · 2021Article
- Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes.eLife · 2021Article
- Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements.PLoS genetics · 2020Review
- Roles of Transposable Elements in the Different Layers of Gene Expression Regulation.International journal of molecular sciences · 2019Review
- Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice.Scientific reports · 2019Article
- Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster.Nucleic acids research · 2019Article
- LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome.Genome research · 2018Article
- Article
- Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses.Genome research · 2018Article
- Article
- Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells.Journal of visualized experiments : JoVE · 2018Article
- Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.Nucleic acids research · 2018Article
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8 authors at 4 institutions in 1 country.
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Abstract
backgroundFunctional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation, and variation in chromatin accessibility across individuals has been linked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained. Furthermore, the processes through which the variation of chromatin accessibility contributes to phenotypic diversity remain poorly understood.
resultsWe profiled chromatin accessibility in liver from seven strains of mice with phenotypic diversity in response to a high-fat/high-sucrose (HF/HS) diet and identified reproducible chromatin variation across the individuals. We found that sites of variable chromatin accessibility were more likely to coincide with particular classes of transposable elements (TEs) than sites with common chromatin signatures. Evolutionarily younger long interspersed nuclear elements (LINEs) are particularly likely to harbor variable chromatin sites. These younger LINEs are enriched for binding sites of immune-associated transcription factors, whereas older LINEs are enriched for liver-specific transcription factors. Genomic region enrichment analysis indicates that variable chromatin sites at TEs may function to regulate liver metabolic pathways. CRISPR-Cas9 deletion of a number of variable chromatin sites at TEs altered expression of nearby metabolic genes. Finally, we show that polymorphism of TEs and differential DNA methylation at TEs can both influence chromatin variation.
conclusionsOur results demonstrate that specific classes of TEs show variable chromatin accessibility across strains of mice that display phenotypic diversity in response to a HF/HS diet. These results indicate that chromatin variation at TEs is an important contributor to phenotypic variation among populations.
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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 Socratic graph.