School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China.
Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518055, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518055, PR China.
Genomics. 2021 Jan;113(1 Pt 1):344-355. doi: 10.1016/j.ygeno.2020.12.026. Epub 2020 Dec 15.
ChIP-seq is widely used for mapping the transcription factor (TF) binding sites throughout the genome in vivo. In this study, we adopted and modified ChIPmentation, a fast, robust, low-input requirement ChIP-seq method, to a transient expression system using soybean protoplasts to expedite the exploration of TF binding sites. To test this new protocol, we expressed a tagged version of a C2H2-type zinc finger TF, JAGGED1 (GmJAG1), in soybean protoplasts and successfully identified its binding sites in the soybean genome. Furthermore, valuable genomic features such as a novel GmJAG1-binding motif, and the epigenetic characteristics as well as an enhancer-like function of GmJBSs were also found via coupling ATAC-seq and H3K27me3 ChIP-seq data. The application of the modified ChIPmentation protocol in this study using soybean protoplasts provided a new approach for rapid elucidation of how a TF binds to the various target genes in the soybean genome, as illustrated here using GmJAG1.
ChIP-seq 被广泛用于在体内绘制整个基因组中转录因子 (TF) 结合位点。在这项研究中，我们采用并改进了 ChIPmentation，这是一种快速、稳健、低输入要求的 ChIP-seq 方法，用于使用大豆原生质体的瞬时表达系统，以加速 TF 结合位点的探索。为了测试这个新方案，我们在大豆原生质体中表达了一个 C2H2 型锌指 TF、JAGGED1（GmJAG1）的标记版本，并成功鉴定了其在大豆基因组中的结合位点。此外，通过结合 ATAC-seq 和 H3K27me3 ChIP-seq 数据，还发现了 GmJAG1 的新型结合基序、表观遗传特征以及 GmJBSs 的增强子样功能等有价值的基因组特征。本研究中使用大豆原生质体对改良 ChIPmentation 方案的应用提供了一种快速阐明 TF 如何与大豆基因组中各种靶基因结合的新方法，这里使用 GmJAG1 进行了说明。
