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Profiling chromatin states using single-cell itChIP-seq
Abstract
Single-cell measurement of chromatin states, including histone modifications and non-histone protein binding, remains challenging. Here, we present a low-cost, efficient, simultaneous indexing and tagmentation-based ChIP-seq (itChIP-seq) method, compatible with both low cellular input and single cells for profiling chromatin states. itChIP combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation within a single tube, enabling the processing of samples from tens of single cells to, more commonly, thousands of single cells per assay. We demonstrate that single-cell itChIP-seq (sc-itChIP-seq) yields ~9,000 unique reads per cell. Using sc-itChIP-seq to profile H3K27ac, we sufficiently capture the earliest epigenetic priming event during the cell fate transition from naive to primed pluripotency, and reveal the basis for cell-type specific enhancer usage during the differentiation of bipotent cardiac progenitor cells into endothelial cells and cardiomyocytes. Our results demonstrate that itChIP is a widely applicable technology for single-cell chromatin profiling of epigenetically heterogeneous cell populations in many biological processes.
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“However, for highly complex adult organs such as the brain, this single-cell characterization has not been achieved.”
From Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues (2021) · cites this paper as [8]
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Metadata
- Authors
- Ai, S., Xiong, H., Li, C. C., Luo, Y., Shi, Q., Liu, Y., Yu, X., Li, C., & He, A.
- Affiliations
- Peking University (CN)
- Corresponding author
- He, Aibin
- Venue
- Nature Cell Biology
- Published
- 2019-09
- Volume
- 21
- Issue
- 9
- Pages
- 1164-1172
- ISSN
- 1465-7392 (ISSN-L)
- 1476-4679
- OpenAlex
- W2972263821
- Cited by
- 140
- References
- 48
- Citations by year
- 2026: 7 · 2025: 15 · 2024: 12 · 2023: 23 · 2022: 23 · 2021: 33 · 2020: 27
- FWCI
- 6.86
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- histone modifications, H3K27ac, epigenetic priming, cardiac progenitor cells, endothelial differentiation, cardiomyocyte differentiation, epigenetic heterogeneity
- MeSH terms
- Animals, Binding Sites, Chromatin, Histones, Mice, Transgenic, Protein Processing, Post-Translational, Sequence Analysis, DNA, Endothelial Cells, Chromatin Immunoprecipitation, Epigenomics
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