Profiling chromatin states using single-cell itChIP-seq
| Autor: | Aibin He, Shanshan Ai, Yaxi Liu, Xianhong Yu, Yingjie Luo, Haiqing Xiong, Cheng Li, Chen Li, Qiang Shi |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Epigenomics
Chromatin Immunoprecipitation Cardiac progenitors genetic processes Cell Mice Transgenic Plasma protein binding Biology Cell fate determination Histones 03 medical and health sciences 0302 clinical medicine medicine Animals natural sciences Epigenetics Enhancer 030304 developmental biology 0303 health sciences Binding Sites Endothelial Cells Cell Biology Sequence Analysis DNA Chromatin Cell biology Histone medicine.anatomical_structure 030220 oncology & carcinogenesis biology.protein Protein Processing Post-Translational |
| Zdroj: | Nature cell biology. 21(9) |
| ISSN: | 1476-4679 |
| Popis: | 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. He and colleagues develop itChIP-seq based on simultaneous cellular indexing and chromatin tagmentation. itChIP-seq is applicable to both low-input and single-cell analyses of chromatin states. |
| Databáze: | OpenAIRE |
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