Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
复制标题
使用 CUT 对棉花中 H3K4me3 修饰进行高效染色质分析
DOI：
10.1186/s13007-020-00664-8
复制
发表时间：
2020-08-31
期刊：
影响因子：
5.1
通讯作者：
Guan, Xueying
中科院分区：
文献类型：
--
作者：
Tao, Xiaoyuan;Feng, Shouli;Guan, Xueying
背景：2019年，Kaya-Okur等人。报道了用于有效分析表观遗传修饰的DNA片段的靶标下切割和标签(Cut&Tag)技术。它主要用于培养细胞系，特别是对小样本和单细胞有效。这一策略产生了高分辨率和低背景噪声的染色质图谱数据，用于表观基因组分析。Cut&Tag非常适合用于植物细胞，特别是在提取小样本的组织中，如胚珠、花药和纤维。结果在这里，我们提出了一种利用植物核的分步切割和标记协议。在该方法中，我们对每个切割和标签反应中可以使用的核进行了量化，并比较了切割和标签与染色质免疫沉淀和测序(CHIP-SEQ)在棉花叶片中的效率。给出了切割标签生物信息学分析的一般流程。结果表明，与CHIP-SEQ相比，CUT&TAG方法速度更快，分辨率更高，背景信号更低。结论利用已分离出的完整细胞核，改进了植物细胞的切割和标记方法。
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.