ArticleNature2015
Single-cell chromatin accessibility reveals principles of regulatory variation.
Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,404 papers.
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Who cites it
1,404 citing papers in PubMed.
- Nuclear mechanotransduction: tools for mechanical perturbation and chromatin characterization.Nucleus (Austin, Tex.) · 2026Review
- Chromatin accessibility shapes development-specific lineage plasticity in hematopoiesis.Blood advances · 2026Article
- Single-cell epigenomics of colorectal cancer.Experimental & molecular medicine · 2026Review
- Genome-wide discovery ofeLife · 2026Article
- The dual-enhanced graph learning framework DePass allows paired data integration in single-cell and spatial multiomics.Nature cell biology · 2026Article
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
- Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.Genome biology and evolution · 2026Article
- Review
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Type 1 interferon perturbates clonal competition by reshaping human blood development.Nature genetics · 2026Article
- Integrated Genomic and Epigenomic Analysis Reveals Epigenetic Plasticity in Disease Progression and Multidrug Resistance in Multiple Myeloma.Cancer research · 2026Article
- GLM-Prior: a genomic language model for transferable sequence-derived priors in gene regulatory network inference.Nature communications · 2026Article
- The development of single-cell lineage tracing technology and its application in immunotherapy.Molecular therapy. Advances · 2026Review
- Multiscale modeling primer: Focus on chromatin and epigenetics.The Journal of biological chemistry · 2026Review
- scGSI: Graph-guided self-supervised integration of paired single-cell multi-omics.PLoS computational biology · 2026Article
- DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator.Interdisciplinary sciences, computational life sciences · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Cohesin acts as a transcriptional gatekeeper by restraining pause-release to promote processive elongation.Nature communications · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- Stimulation of Adult Muscle Stem Cells with BMPs Results in Direct Activation of Notch Pathway Genes.Cells · 2026Article
1,344 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. Although recent advances have improved our ability to document cellular phenotypic variation, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the 'regulome'.
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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.