ArticleMolecular systems biology2020
Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Sensory receptor expansion and neural accommodation in butterfly color vision.Science advances · 2026Article
- NADThe EMBO journal · 2026Article
- Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.Cell reports. Medicine · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Expanding the fly eye gene regulatory network: From Drosophila to the hoverfly Episyrphus balteatus.PLoS genetics · 2026Article
- Sensory receptor expansion and neural accommodation in butterfly color vision.bioRxiv : the preprint server for biology · 2025Article
- Hemocytes facilitate interclonal cooperation-induced tumor malignancy by hijacking the innate immune system in Drosophila.The EMBO journal · 2025Article
- Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis.Nature communications · 2025Article
- Divergent combinations of enhancers encode spatial gene expression.Nature communications · 2025Article
- FrozONE: quick cell nucleus enrichment for comprehensive proteomics analysis of frozen tissues.Life science alliance · 2025Article
- Molecular profiling of invertebrate glia.Glia · 2025Review
- GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data.Bioinformatics (Oxford, England) · 2024Article
- Gene regulatory networks in disease and ageing.Nature reviews. Nephrology · 2024Review
- Synergistic activation by Glass and Pointed promotes neuronal identity in the Drosophila eye disc.Nature communications · 2024Article
- Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine.Military Medical Research · 2024Review
- Article
- Decoding mutational hotspots in human disease through the gene modules governing thymic regulatory T cells.Frontiers in immunology · 2024Article
- Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation.Nature cell biology · 2024Article
- Review
- A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines.Nature communications · 2023Article
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14 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.