Interactions of enhancers with promoters and transcription factors mediate chromatin loop formation to regulate downstream gene expression in response to environmental stimuli such as light.

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.

Plant cis-regulatory sequences (CRSs) are essential for gene expression and transcriptional regulation in plants. With the rapid development of plant biotechnologies, such as transgenesis and gene editing tools, plant-derived CRSs have gradually replaced traditional CRSs, like the 35S promoter, to avoid some negative effects caused by exogenous DNA sequences. In this study, we provided a comprehensive analysis of the published genomic data of Andrographis paniculata and identified six candidate ApACRs. Based on the transient assays, two candidate CRSs (ApACR1 and ApACR2) demonstrated high transcriptional activities comparable to those of the 35S promoter in several plant species, in contrast to others with lower activities, suggesting their further potential applications in plant biotechnology and genetic engineering.

Andrographolide (AD) is the major bioactive component in the Chinese medicinal plant Andrographis paniculata (A. paniculata), which is widely used for its anti-inflammatory and antiviral properties. In this study, we observed that light is a critical environmental factor for AD biosynthesis and identified a potential transcription factor, ApTrihelix1, as a regulator of AD biosynthesis via RNA-seq combined with co-expression analysis. ApTrihelix1 is light-induced, and knocking down its expression downregulates AD content as well as the expression of several AD biosynthesis-related genes (ADRGs). Furthermore, through high-throughput sequencing methods (e.g. ChIP-seq) and molecular experiments (e.g. Yeast One Hybrid assay), ApTrihelix1 was found to bind to the promoter of ApCPS2 (a key ADRG) to activate its expression. Taken together, these data strongly support that light upregulates the expression of certain transcription factors (e.g. ApTrihelix1), thereby activating key ADRGs (e.g. ApCPS2) and promoting AD accumulation in A. paniculata.

Transcription factors function in complex regulatory networks to regulate various biological and physiological processes. In soybean (Glycine max), GmLUX, as an important component of the evening complex, plays a critical role in the regulation of soybean flowering regulation. In this study, the genome-wide characterization and epigenetic features of GmLUX binding sites have been analyzed using high-throughput sequencing methods, such as ChIP-seq, Hi-C, histone modification and ATAC-seq. In addition, combined with molecular experiments, GmLUX was found to be able to directly regulate the CO-like gene by facilitating chromatin interactions, suggesting a new regulatory pathway of GmLUX in controlling flowering, which provided the important genomic resources for a further understanding of its regulatory mechanism.