ArticleNucleic acids research2017
Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
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- Heparin-Binding Hemagglutinin-Induced Trained Immunity in Macrophages: Implications for Antimycobacterial Defense.Biomolecules · 2025Article
- Epigenetic Modifications in the Retinal Pigment Epithelium of the Eye During RPE-Related Regeneration or Retinal Diseases in Vertebrates.Biomedicines · 2025Review
- Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states.Nucleic acids research · 2025Article
- RBM25 is required to restrain inflammation via ACLY RNA splicing-dependent metabolism rewiring.Cellular & molecular immunology · 2024Article
- H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.bioRxiv : the preprint server for biology · 2024Article
- The histone methyltransferase ASH1L protects against bone loss by inhibiting osteoclastogenesis.Cell death and differentiation · 2024Article
- The chromatin signatures of enhancers and their dynamic regulation.Nucleus (Austin, Tex.) · 2023Review
- Prognosis of colon cancer patients based on enhancer RNAs-related genes.Journal of cancer research and clinical oncology · 2023Article
- Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair.Nucleic acids research · 2023Article
- Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A.Nucleic acids research · 2022Article
- Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era.Journal of proteome research · 2021Review
- Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes.Nucleic acids research · 2020Article
- Epigenetic Regulation of S100A9 and S100A12 Expression in Monocyte-Macrophage System in Hyperglycemic Conditions.Frontiers in immunology · 2020Article
- Epigenetic regulation of renal development.Seminars in cell & developmental biology · 2019Review
- Lysine-Specific Histone Demethylase 1A Regulates Macrophage Polarization and Checkpoint Molecules in the Tumor Microenvironment of Triple-Negative Breast Cancer.Frontiers in immunology · 2019Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type-specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K4me1/K36me2 marks transcribed enhancers, while H3K4me1/K36me3 and H3K4me1/K79me2 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.
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