ArticleNucleic acids research2015
Modeling the relationship of epigenetic modifications to transcription factor binding.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 108 citations in OpenAlex.
- EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.Briefings in bioinformatics · 2026Article
- H2AK119ub dynamics control hair follicle stem cell quiescence.Nature communications · 2025Article
- Up-regulation of blood-circulating TIM-4-expressing monocytes and potential diagnostic biomarker sTIM-4 in primary liver cancer.Scientific reports · 2025Article
- Elevated EGR1 binding at enhancers in excitatory neurons correlates with neuronal subtype-specific epigenetic regulation.BMC biology · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- Dissecting cardiovascular disease-associated noncoding genetic variants using human iPSC models.Stem cell reports · 2025Review
- Article
- Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states.Briefings in bioinformatics · 2024Article
- Schlank orchestrates insect developmental transition by switching H3K27 acetylation to trimethylation in the prothoracic gland.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants.Genome biology · 2023Article
- GoPeaks: histone modification peak calling for CUT&Tag.Genome biology · 2022Article
- Asymmetric Predictive Relationships Across Histone Modifications.Nature machine intelligence · 2022Article
- CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells for myocardial infarction therapy.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Integrated Analysis of Gene Expression and Methylation Data to Identify Potential Biomarkers Related to Atherosclerosis Onset.Oxidative medicine and cellular longevity · 2022Article
- STAT1 epigenetically regulates LCP2 and TNFAIP2 by recruiting EP300 to contribute to the pathogenesis of inflammatory bowel disease.Clinical epigenetics · 2021Article
- CpG content-dependent associations between transcription factors and histone modifications.PloS one · 2021Article
- An Update in Epigenetics in Metabolic-Associated Fatty Liver Disease.Frontiers in medicine · 2021Review
- Epigenetic Regulation of Vascular Smooth Muscle Cell Phenotype Switching in Atherosclerotic Artery Remodeling: A Mini-Review.Frontiers in genetics · 2021Review
- Article
- Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis.International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Transcription factors (TFs) and epigenetic modifications play crucial roles in the regulation of gene expression, and correlations between the two types of factors have been discovered. However, methods for quantitatively studying the correlations remain limited. Here, we present a computational approach to systematically investigating how epigenetic changes in chromatin architectures or DNA sequences relate to TF binding. We implemented statistical analyses to illustrate that epigenetic modifications are predictive of TF binding affinities, without the need of sequence information. Intriguingly, by considering genome locations relative to transcription start sites (TSSs) or enhancer midpoints, our analyses show that different locations display various relationship patterns. For instance, H3K4me3, H3k9ac and H3k27ac contribute more in the regions near TSSs, whereas H3K4me1 and H3k79me2 dominate in the regions far from TSSs. DNA methylation plays relatively important roles when close to TSSs than in other regions. In addition, the results show that epigenetic modification models for the predictions of TF binding affinities are cell line-specific. Taken together, our study elucidates highly coordinated, but location- and cell type-specific relationships between epigenetic modifications and binding affinities of TFs.
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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.