ArticleNature genetics2023
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
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Who cites it
170 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- 3D Genome Engineering Using CRISPR/dCas Systems.International journal of molecular sciences · 2026Review
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- HiCPotts: an R/bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias.Bioinformatics (Oxford, England) · 2026Article
- Diverse Roles of Cohesin in Chromosome Dynamics and Stem Cells.Biotech (Basel (Switzerland)) · 2026Review
- Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.Cell genomics · 2026Article
- Transcription factors as drivers of 3D enhancer-promoter interactions.Current opinion in structural biology · 2026Review
- Promoter strength and position govern promoter competition through transcript-dependent insulation.Nature genetics · 2026Article
- High-resolution chromatin mapping reveals that CTCF anchors meiotic loops to the chromosome axis.Nature communications · 2026Article
- HiC2Self: Self-supervised denoising for bulk and single-cell Hi-C contact maps.Science advances · 2026Article
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- Shared binding sites for the chromosomal architectural protein Su(Hw) mediate physical interactions betweenbioRxiv : the preprint server for biology · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Functional and computational interrogation of juvenile idiopathic arthritis risk loci in CD4+ T cells.HGG advances · 2026Article
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.bioRxiv : the preprint server for biology · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
- Article
110 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Although enhancers are central regulators of mammalian gene expression, the mechanisms underlying enhancer-promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale three-dimensional (3D) genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining micrococcal nuclease (MNase)-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of ~317 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters, and although loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may partially explain why acute cohesin depletion only modestly affects global gene expression.
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