ArticleNature biotechnology2022
Single-cell measurement of higher-order 3D genome organization with scSPRITE.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 131 citations in OpenAlex.
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- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.Nature communications · 2026Article
- Transcription condensates are promoter hubs that enhance transcriptional bursts.bioRxiv : the preprint server for biology · 2026Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- Recurrence plot reconstruction reveals chromosomal reorganization before territory formation.NAR genomics and bioinformatics · 2026Article
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Harmonizing single-cell 3D genome data with STARK and scNucleome.Genome biology · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
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- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq).Nature communications · 2025Article
- Clinical application of single-cell RNA sequencing in disease and therapy.Clinical and translational medicine · 2025Review
- Advancing biological understanding of cellular senescence with computational multiomics.Nature genetics · 2025Review
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
29 more citing papers are in PubMed but not listed here.
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9 authors at 1 institution in 1 country.
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Abstract
Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.
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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 OpenQuestion graph.