4.6 Article

Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag

Journal

PLANT METHODS
Volume 16, Issue 1, Pages -

Publisher

BMC
DOI: 10.1186/s13007-020-00664-8

Keywords

Cut&Tag; Cotton; ChIP

Funding

  1. National Key Research and Development Program [2016YFD0100605]
  2. National Natural Science Foundation of China (NSFC) [31971985, 31900395]
  3. China Postdoctoral Science Foundation [2018M632477, 2019M652094]
  4. Dabeinong Funds for Discipline Development and Talent Training in Zhejiang University
  5. Fundamental Research Funds for the Central Universities
  6. JCIC-MCP project

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Background In 2019, Kaya-Okur et al. reported on the cleavage under targets and tagmentation (CUT&Tag) technology for efficient profiling of epigenetically modified DNA fragments. It was used mainly for cultured cell lines and was especially effective for small samples and single cells. This strategy generated high-resolution and low-background-noise chromatin profiling data for epigenomic analysis. CUT&Tag is well suited to be used in plant cells, especially in tissues from which small samples are taken, such as ovules, anthers, and fibers. Results Here, we present a CUT&Tag protocol step by step using plant nuclei. In this protocol, we quantified the nuclei that can be used in each CUT&Tag reaction, and compared the efficiency of CUT&Tag with chromatin immunoprecipitation with sequencing (ChIP-seq) in the leaves of cotton. A general workflow for the bioinformatic analysis of CUT&Tag is also provided. Results indicated that, compared with ChIP-seq, the CUT&Tag procedure was faster and showed a higher-resolution, lower-background signal than did ChIP. Conclusion A CUT&Tag protocol has been refined for plant cells using intact nuclei that have been isolated.

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