ArticleNature biotechnology2025
Tracking single-cell evolution using clock-like chromatin accessibility loci.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- CellRank: consistent and data view agnostic fate mapping for single-cell genomics.Nature protocols · 2026Review
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics.Nature communications · 2026Article
- The Use of Single-Cell Mitochondrial DNA SNP Combinations for Distinguishing Organ-Specific Cell Types.Cells · 2026Article
- Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT.Nature communications · 2026Article
- Mitochondrial-Endothelial Crosstalk in Cardiometabolic Disease: Mechanisms and Translational Opportunities in the Multi-omics Era.Reviews in cardiovascular medicine · 2026Review
- Epigenetic insights into minimal residual disease detection in cancer.Genes & diseases · 2026Article
- Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.Nature aging · 2026Article
- Heterogeneity and Clinical Relevance of Human Adipose Stromal and Progenitor Cells.Diabetes & metabolism journal · 2026Review
- Immune Ageing Clocks: A Methods-Oriented Review of Tasks, Modalities, Models, and Recalibration.Cells · 2026Review
- A Manifold-Based Measure of Transcriptional Entropy for Quantifying Aging in Single Cells.bioRxiv : the preprint server for biology · 2026Article
- Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.Nucleic acids research · 2026Article
- A candidate PPARγ to GPX4 axis in ferroptosis suppression and platinum resistance in bladder cancer: evidence appraisal and a testable research agenda.Journal of Cancer · 2026Review
- Evolution of Cancer Metastases via Lineage Trans-Differentiation.Research (Washington, D.C.) · 2026Article
- Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.Bioengineering (Basel, Switzerland) · 2025Review
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
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10 authors.
Funding
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Abstract
Single-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Previous studies showed age-associated DNA methylation (DNAm) changes in specific genomic regions, termed clock-like differential methylation loci (ClockDML). Age-associated DNAm could either result from or result in chromatin accessibility changes at ClockDML. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. In this study, we developed a method, called EpiTrace, that counts the fraction of opened clock-like loci from scATAC-seq data to determine cell age and perform lineage tracing in various cell lineages and animal species. It shows concordance with known developmental hierarchies, correlates well with DNAm-based clocks and is complementary with mutation-based lineage tracing, RNA velocity and stemness predictions. Applying EpiTrace to scATAC-seq data reveals biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification.
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