ArticleProceedings of the National Academy of Sciences of the United States of America2022
Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 19 citations in OpenAlex.
- Profiling chromatin accessibility responses to seasonal heat stress in Angora rabbit testes.BMC genomics · 2026Article
- Targeting the 3D genome by anthracyclines for chemotherapeutic effects.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis.Genome biology · 2025Article
- Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.Nature genetics · 2025Article
- Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice.Nature methods · 2024Article
- A machine-readable specification for genomics assays.Bioinformatics (Oxford, England) · 2024Article
- Estimating and Assessing Differential Equation Models with Time-Course Data.The journal of physical chemistry. B · 2023Article
- Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) and its coassays have transformed the field of single-cell epigenomics and transcriptomics. However, the low detection efficiency of current methods has limited our understanding of the true complexity of chromatin accessibility and its relationship with gene expression in single cells. Here, we report a high-sensitivity scATAC-seq method, termed multiplexed end-tagging amplification of transposase accessible chromatin (METATAC), which detects a large number of accessible sites per cell and is compatible with automation. Our high detectability and statistical framework allowed precise linking of enhancers to promoters without merging single cells. We systematically investigated allele-specific accessibility in the mouse cerebral cortex, revealing allele-specific accessibility of promotors of certain imprinted genes but biallelic accessibility of their enhancers. Finally, we combined METATAC with our high-sensitivity single-cell RNA sequencing (scRNA-seq) method, multiple annealing and looping based amplification cycles for digital transcriptomics (MALBAC-DT), to develop a joint ATAC-RNA assay, termed METATAC and MALBAC-DT coassay by sequencing (M2C-seq). M2C-seq achieved significant improvements for both ATAC and RNA compared with previous methods, with consistent performance across cell lines and early mouse embryos.
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