An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts

Mingkun Huang, Ling Zhang, Limeng Zhou, Mozhu Wang, Wai-Shing Yung, Zhili Wang, Shaowei Duan, Zhixia Xiao, Qianwen Wang, Xin Wang, Man-Wah Li, Hon-Ming Lam

Genomics; 2021 Jan;113(1 Pt 1):344-355.  doi: 10.1016/j.ygeno.2020.12.026.

Abstract

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.

See https://pubmed.ncbi.nlm.nih.gov/33338631/

Figure 1:

Overview of GmJAG1 enrichment in the soybean W82 genome by ChIP-seq. A view of GmJAG1 ChIP-seq data (inner circle, blue), GmJAG1 gene target densities (middle circle, red), transposable element (TE) densities (outer circle, black), and 200 representative GmJAG1-associated paralogous gene pairs (center links, yellow) was shown. Genes harboring GmJAG1 enrichment signal within the 2-kb promoter region were referred as the GmJAG1 targeted genes. Transposable element region was download from the Phytozome database. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)