An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Open accessAbstract
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.
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Compared to prior single-cell multiomics sequencing methods for joint RNA and epigenome analyses, Paired-Damage-seq displayed similar sensitivity in RNA detection.
“Compared to prior single-cell multiomics sequencing methods for joint RNA and epigenome analyses27,39–41, Paired-Damage-seq displayed similar sensitivity in RNA detection, despite different DNA modalities being measured”
From Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability (2025) · cites this paper as [39]
Milo may also be useful for single-cell assays beyond scRNA-seq, including multi-omic assays.
“Milo may also be applicable to single-cell assays other than scRNA-seq, including multi-omic assays [35–39].”
From Differential abundance testing on single-cell data using k-nearest neighbor graphs (2022) · cites this paper as [38]
Joint snRNA-seq and snATAC-seq on more than 15,000 fetal and adult mouse cortical cells showed dynamic, cell-type-specific changes in promoter accessibility during development.
“Paired snRNA-seq and snATAC-seq of over 15,000 cells in fetal and adult mouse cortex revealed cell type-specific dynamic regulation of promoter accessibility during brain development (Chen et al., 2019b; Zhu et al., 2019).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Zhu et al., 2019
In mouse cerebral cortex, high-throughput multi-omics detected only 9-22 cell types, whereas scRNA-seq detected more than 100.
“As a result, high-throughput multi-omics studies in mouse cerebral cortex identified 9–22 cell types (Chen et al., 2019b; Zhu et al., 2019), compared with over 100 cell types found using scRNA-seq (Tasic et al., 2018; Yao et al., 2020a, 2020b).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Zhu et al., 2019
Paired-seq used three rounds of ligation-based combinatorial indexing to process 1 million nuclei in a single experiment for parallel transcriptome and chromatin accessibility analyses.
“This strategy was implemented shortly after by Paired-seq, which used three rounds of ligation-based combinatorial indexing to process 1 million nuclei in a single experiment for parallel transcriptome and chromatin accessibility analyses59.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [59]
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Self-citation
- Authors
- Zhu, C., Yu, M., Huang, H., Juric, I., Abnousi, A., Hu, R., Lucero, J., Behrens, M. M., Hu, M., & Ren, B.
- Affiliations
- Ludwig Cancer Research (US)
- University of California San Diego (US)
- Cleveland Clinic (US)
- Salk Institute for Biological Studies (US)
- Corresponding author
- Ren, Bing
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2019-11
- Volume
- 26
- Issue
- 11
- Pages
- 1063-1070
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC7231560
- OpenAlex
- W2985765936
- Cited by
- 344
- References
- 71
- Citations by year
- 2026: 30 · 2025: 47 · 2024: 56 · 2023: 66 · 2022: 56 · 2021: 56 · 2020: 31 · 2019: 1
- FWCI
- 11.91
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of Mental Health (U19MH114831)
- National Human Genome Research Institute (U54HG006997)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- single-cell transcriptomics, chromatin accessibility, open chromatin, enhancer target genes, gene regulatory programs, forebrain development, cerebral cortex
- MeSH terms
- Animals, Brain, Chromatin, Humans, Male, Mice, Inbred C57BL, Gene Expression Profiling, NIH 3T3 Cells, Mice, Hep G2 Cells, HEK293 Cells, Single-Cell Analysis, Transcriptome
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