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.
Genomics, 2021/01;113(1 Pt 1):344-355.
Huang M[1], Zhang L[2], Zhou L[1], Wang M[1], Yung WS[1], Wang Z[1], Duan S[1], Xiao Z[1], Wang Q[1], Wang X[1], Li MW[1], Lam HM[3]
Affiliations
PMID: 33338631DOI: 10.1016/j.ygeno.2020.12.026
Impact factor: 4.31
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.
Keywords: ATAC-seq; ChIP-seq; Enhancer; JAG1; Motif; Soybean
MeSH terms
Chromatin Assembly and Disassembly; Gene Expression Regulation, Plant; Genome, Plant; Jagged-1 Protein; Nucleotide Motifs; Plant Proteins; Promoter Regions, Genetic; Protein Binding; Protoplasts; Glycine max
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