期刊
GENOMICS
卷 113, 期 1, 页码 344-355出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2020.12.026
关键词
Soybean; JAG1; Motif; ChIP-seq; ATAC-seq; Enhancer
资金
- Hong Kong Research Grants Council Area of Excellence Scheme [AoE/M-403/16]
- Lo Kwee-Seong Biomedical Research Fund
- Impact Postdoctoral Fellowship Scheme of The Chinese University of Hong Kong
In this study, the modified ChIPmentation protocol was successfully used in soybean protoplasts to identify binding sites of the C2H2-type zinc finger TF GmJAG1. Furthermore, a novel GmJAG1-binding motif, epigenetic characteristics, and enhancer-like function of GmJBSs were also discovered.
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.
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