ArticleCell genomics2023
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- EpiATLAS - a reference for human epigenomic research.bioRxiv : the preprint server for biology · 2026Article
- Distinguishing causal from tagging enhancers using single-cell multiome data.medRxiv : the preprint server for health sciences · 2026Article
- Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.Nature communications · 2026Article
- Article
- MultiGATE: integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning.Nature communications · 2025Article
- Targeting eRNA-Producing Super-Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient-Derived Immune Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues.Nucleic acids research · 2025Article
- Article
- Toll-Interacting Protein Down-Regulation by Cigarette Smoke Exposure Impairs Human Lung Defense against Influenza A Virus Infection.The American journal of pathology · 2025Article
- Article
- Chromatin State Maps of Blood Pressure-Relevant Renal Segments Reveal Potential Regulatory Role for SNPs.Hypertension (Dallas, Tex. : 1979) · 2025Article
- GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data.Bioinformatics (Oxford, England) · 2024Article
- Enhlink infers distal and context-specific enhancer-promoter linkages.Genome biology · 2024Article
- Article
- Droplet-based single-cell joint profiling of histone modifications and transcriptomes.Nature structural & molecular biology · 2023Article
- Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain.bioRxiv : the preprint server for biology · 2023Article
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19 authors.
Funding
Abstract
Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.
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