ArticleProceedings of the National Academy of Sciences of the United States of America2019
Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 50 citations in OpenAlex.
- Population-level Variability in Genome-wide Repressive Histone Marks in a Fungal Wheat Pathogen.Genome biology and evolution · 2026Article
- Machine and Deep Learning Reveal Sequence Determinants Encoding Bivalent Histone Modifications.Communications biology · 2026Article
- Identification of novel DNA sequence motifs that modulate transcription in T cells.BMC genomics · 2026Article
- Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.Cell proliferation · 2025Article
- Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants.Journal of virology · 2025Article
- Interpretable prediction of mRNA abundance from promoter sequence using contextual regression models.NAR genomics and bioinformatics · 2024Article
- Epigenetic Modulation of GPER Expression in Gastric and Colonic Smooth Muscle of Male and Female Non-Obese Diabetic (NOD) Mice: Insights into H3K4me3 and H3K27ac Modifications.International journal of molecular sciences · 2024Article
- ALKHB5-demethylated lncRNA SNHG15 promotes myeloma tumorigenicity by increasing chromatin accessibility and recruiting H3K36me3 modifier SETD2.American journal of physiology. Cell physiology · 2024Article
- Deep Resequencing of the 1q22 Locus in Non-Lobar Intracerebral Hemorrhage.Annals of neurology · 2024Article
- CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nature communications · 2023Article
- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
- Multimodal learning of noncoding variant effects using genome sequence and chromatin structure.Bioinformatics (Oxford, England) · 2023Article
- Histone Maps inInternational journal of molecular sciences · 2023Article
- Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock.Genome research · 2023Article
- How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances.Pharmaceutics · 2022Review
- Identification of essential element determining fruit-specific transcriptional activity in the tomato HISTIDINE DECARBOXYLASE A gene promoter.Plant cell reports · 2022Article
- Asymmetric Predictive Relationships Across Histone Modifications.Nature machine intelligence · 2022Article
- Global Gene Expression Regulation Mediated by TGFβ Through H3K9me3 Mark.Cancer informatics · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Deciphering the genetic code of DNA methylation.Briefings in bioinformatics · 2021Review
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Histones are modified by enzymes that act in a locus, cell-type, and developmental stage-specific manner. The recruitment of enzymes to chromatin is regulated at multiple levels, including interaction with sequence-specific DNA-binding factors. However, the DNA-binding specificity of the regulatory factors that orchestrate specific histone modifications has not been broadly mapped. We have analyzed 6 histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3, K3H9me3, H3K36me3) across 121 human cell types and tissues from the NIH Roadmap Epigenomics Project as well as 8 histone marks (with addition of H3K4me2 and H3K9ac) from the mouse ENCODE Consortium. We have identified 361 and 369 DNA motifs in human and mouse, respectively, that are the most predictive of each histone mark. Interestingly, 107 human motifs are conserved between the two species. In human embryonic cell line H1, we mutated only the found DNA motifs at particular loci and the significant reduction of H3K27ac levels validated the regulatory roles of the perturbed motifs. The functionality of these motifs was also supported by the evidence that histone-associated motifs, especially H3K4me3 motifs, significantly overlap with the expression of quantitative trait loci SNPs in cancer patients more than the known and random motifs. Furthermore, we observed possible feedbacks to control chromatin dynamics as the found motifs appear in the promoters or enhancers associated with various histone modification enzymes. These results pave the way toward revealing the molecular mechanisms of epigenetic events, such as histone modification dynamics and epigenetic priming.
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