Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression
Open accessAbstract
Methods for quantifying gene expression 1 and chromatin accessibility 2 in single cells are well established, but single-cell analysis of chromatin regions with specific histone modifications has been technically challenging. In this study, we adapted the CUT&Tag method 3 to scalable nanowell and droplet-based single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues and during the differentiation of human embryonic stem cells. We focused on profiling polycomb group (PcG) silenced regions marked by histone H3 Lys27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we used scCUT&Tag to profile H3K27me3 in a patient with a brain tumor before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.
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High chromatin silencing score indicates repressed gene expression because of the transcriptional repression function of H3K27me3.
“High CSS indicates repressed gene expression because of the transcriptional repression function of H3K27me3.”
From Spatial epigenome–transcriptome co-profiling of mammalian tissues (2023) · cites this paper as [35]
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References 29 · Cited by 201
- Authors
- Wu, S. J., Furlan, S. N., Mihalas, A. B., Kaya-Okur, H. S., Feroze, A. H., Emerson, S. N., Zheng, Y., Carson, K., Cimino, P. J., Keene, C. D., Sarthy, J. F., Gottardo, R., Ahmad, K., Henikoff, S., & Patel, A. P.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Fred Hutch Cancer Center (US)
- Corresponding author
- Henikoff, Steven
- Patel, Anoop P.
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2021-04-12
- Volume
- 39
- Issue
- 7
- Pages
- 819-824
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC8277750
- OpenAlex
- W3152578692
- Cited by
- 201
- References
- 29
- Citations by year
- 2026: 33 · 2025: 30 · 2024: 35 · 2023: 44 · 2022: 39 · 2021: 20
- FWCI
- 10.82
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- American Cancer Society
- U.S. Department of Health & Human Services | National Institutes of Health (CA245037, GM10869)
- Howard Hughes Medical Institute
- Chan-Zuckerberg Initiative
- Burroughs Wellcome Fund
- 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 › Epigenetics and DNA Methylation
- Keywords
- histone modifications, H3K27me3, Polycomb group proteins, chromatin accessibility, human embryonic stem cell differentiation, tumor microenvironment, brain tumors, cell type annotation
- MeSH terms
- Brain Neoplasms, Cell Differentiation, Chromatin, Gene Expression Regulation, Humans, K562 Cells, Gene Silencing, Embryonic Stem Cells, Jumonji Domain-Containing Histone Demethylases, Single-Cell Analysis, Polycomb-Group Proteins
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