Cited by 141Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomicsEpigenetics and DNA Methylation

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Profiling chromatin states using single-cell itChIP-seq

Ai, Shanshan, Xiong, Haiqing, Li, Chen C., Luo, Yingjie, Shi, Qiang, Liu, Yaxi, Yu, Xianhong, Li, Cheng, He, Aibin·2019·Nature Cell Biology

DOI 10.1038/s41556-019-0383-5

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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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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
ORCID: Ai, Shanshan
Xiong, Haiqing
Li, Chen C.
Luo, Yingjie
Shi, Qiang
Liu, Yaxi
Li, Cheng
He, Aibin
Venue: Nature Cell Biology
Publisher: Springer Science and Business Media LLC
Published: 2019-09
Volume: 21
Issue: 9
Pages: 1164-1172
ISSN: 1465-7392 (ISSN-L)
1476-4679
DOI: 10.1038/s41556-019-0383-5
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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Profiling chromatin states using single-cell itChIP-seq

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