Journal
GENOMICS
Volume 113, Issue 1, Pages 344-355Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2020.12.026
Keywords
Soybean; JAG1; Motif; ChIP-seq; ATAC-seq; Enhancer
Funding
- 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
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available