How noncoding open chromatin regions shape soybean domestication

Huang, Mingkun; Li, Man-Wah; Lam, Hon‐Ming

doi:10.1016/j.tplants.2021.06.008

Cited by 3 publications

(1 citation statement)

References 11 publications

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“…In contrast to human or model plants (e.g., Arabidopsis), there are many databases with abundant sequencing data for understanding the function of noncoding regions, such as the human ENCODE (https://www.encodeproject.org accessed on 1 May 2024) and the Arabidopsis Cistrome database [20]. Although soybean also has abundant DNA resequencing data characterizing the single nucleotide polymorph (SNP) or structural variation (SV) at the genomic level, for example, the recently published soybean PAN-genome data [21], few high-throughput sequencing data (e.g., ATAC-seq) [22][23][24] have been aimed at finding these functional non-coding elements (e.g., motifs) in the soybean genome. Compared to the ChIP-seq method [14], a traditional strategy for discovering new motifs, DAP-seq [15] is able to select the DNA fragments directly bound by the recombinant TF in vitro, which showed some advantage over the ChIP-seq in finding motifs.…”

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confidence: 99%

Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq

Wang,

Pu,

Zhang

et al. 2024

Plants

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Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.

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