ArticleNature methods2024
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice.
Article in Nature methods, 2024. 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.
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- Olfactory epithelium regeneration and homeostasis: cellular and molecular mechanisms and novel methodological advances.Cell regeneration (London, England) · 2026Review
- A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain.Cell · 2026Article
- Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- CellLoop: Identifying single-cell 3D genome chromatin loops.Nature communications · 2026Article
- Delta family protocadherins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb.PLoS genetics · 2026Article
- Enhancer Dynamics for Gene Regulation in the Cardiovascular System.Arteriosclerosis, thrombosis, and vascular biology · 2026Review
- Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR.Nature biotechnology · 2026Article
- Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data.Nature communications · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- Harmonizing single-cell 3D genome data with STARK and scNucleome.Genome biology · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- From cellular heterogeneity to precision medicine: single-cell multi-omics in CNS disease research.Frontiers in cellular neuroscience · 2026Review
- An epigenetic repressor TRIM66 dictates monogenic olfactory receptor expression, neural activity, and olfactory behavior.Nature communications · 2025Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.bioRxiv : the preprint server for biology · 2025Article
- Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells.Nature structural & molecular biology · 2025Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding a genome's structure-function relationship, yet this is challenging for existing methods. Here we present 'Linking mRNA to Chromatin Architecture (LiMCA)', which jointly profiles the 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we successfully characterized chromatin accessibility, as well as paired 3D genome structures and gene expression information, of individual developing olfactory sensory neurons. We expanded the repertoire of known olfactory receptor (OR) enhancers and discovered unexpected rules of their dynamics: OR genes and their enhancers are most accessible during early differentiation. Furthermore, we revealed the dynamic spatial relationship between ORs and enhancers behind stepwise OR expression. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the 'one neuron-one receptor' selection process.
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