ArticleNature communications2023
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- 3D epigenomic landscape of the human retinal pigment epithelium.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- Multidimensional mapping of stimulation-responsive regulatory elements and candidate causal variants in T cell activation.Science advances · 2026Article
- Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcription.Cancer cell · 2025Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan.Nature methods · 2025Article
- Coupling the 3D epigenome to the transcriptome in single cells.Nature methods · 2025Article
- BL-Hi-C reveals the 3D genome structure ofHorticulture research · 2024Article
- 3D genome perspective on cell fate determination, organ regeneration, and diseases.Cell proliferation · 2023Review
- A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling.PloS one · 2023Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
Connecting genes to their cis-regulatory elements has been enabled by genome-wide mapping of chromatin interactions using proximity ligation in ChIA-PET, Hi-C, and their derivatives. However, these methods require millions of input cells for high-quality data and thus are unsuitable for many studies when only limited cells are available. Conversely, epigenomic profiling via transposase digestion in ATAC-seq requires only hundreds to thousands of cells to robustly map open chromatin associated with transcription activity, but it cannot directly connect active genes to their distal enhancers. Here, we combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq into ChIATAC to efficiently map interactions between open chromatin loci in low numbers of input cells. We validate ChIATAC in Drosophila cells and optimize it for mapping 3D epigenomes in human cells robustly. Applying ChIATAC to primary human T cells, we reveal mechanisms that topologically regulate transcriptional programs during T cell activation.
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