ArticleNucleic acids research2017
Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture.
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 95 papers.
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Who cites it
95 citing papers in PubMed.
- Insulators As Dynamic, Tunable Regulators of Enhancer-Promoter Coordination in LivingbioRxiv : the preprint server for biology · 2026Article
- 3D genome organization in tissue regeneration involves long-range chromatin loops.Science advances · 2026Article
- Nuclear exosome targeting complexes modulate cohesin binding and enhancer-promoter interactions in 3D.Nature communications · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- Cooperation between architectural C2H2 proteins in CP190 recruitment to Drosophila regulatory elements.Epigenetics & chromatin · 2025Article
- ZAD mediates chromatin binding and insulator activity of Drosophila Pita and can be replaced with the human ZFP276 ZAD-like domain.Epigenetics & chromatin · 2025Article
- Chromatin insulators in gene regulation and 3D genome organization.Biochemical Society transactions · 2025Review
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Insulator BEAF32 regulates expression of tissue-specific genes and piRNA source loci in Drosophila ovaries.Epigenetics & chromatin · 2025Article
- The homie insulator has sub-elements with different insulating and long-range pairing properties.Genetics · 2025Article
- Drosophila architectural proteins M1BP and Opbp cooperatively form the active promoter of a ribosomal protein gene.Epigenetics & chromatin · 2025Article
- ThebioRxiv : the preprint server for biology · 2025Article
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.NAR genomics and bioinformatics · 2024Article
- Development and evolution of Drosophila chromatin landscape in a 3D genome context.Nature communications · 2024Article
- New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity.Nucleic acids research · 2024Article
- The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization.Nucleic acids research · 2024Article
- Mechanistic drivers of chromatin organization into compartments.Current opinion in genetics & development · 2024Review
- Article
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.bioRxiv : the preprint server for biology · 2024Article
- Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.iScience · 2024Article
35 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions. hkCP enhancers contain H3K4me3 and exclusively bind Cap-H2, Chromator, DREF and Z4, whereas dCP enhancers contain H3K4me1 and are more enriched for Rad21 and Fs(1)h-L. Additionally, we map the interactions of each enhancer class utilizing a Hi-C dataset with <1 kb resolution. Results suggest that hkCP enhancers are more likely to form multi-TSS interaction networks and be associated with topologically associating domain (TAD) borders, while dCP enhancers are more often bound to one or two TSSs and are enriched at chromatin loop anchors. The data support a model suggesting that the unique architectural protein occupancy within enhancers is one contributor to enhancer-promoter interaction specificity.
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