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.

Chromatin accessibility is important for genome architecture and gene expression in plants. In this study, the ATAC-seq method was utilized to identify accessible chromatin regions (ACRs) across the chickpea (Cicer arietinum) genome, an important legume crop cultivated worldwide. A total of 11,555 ACRs were identified in the chickpea genome, enriched at gene transcription start sites (TSS) and positively correlated with gene expression. Furthermore, as expected, a number of known transcription factor (TF) binding motifs were enriched in these ACRs. Integrating histone modification data, ACRs were found to be closely associated with H3K27ac and H3K4me3 modifications to regulate gene expression. In addition, the gain and loss of ACRs have been demonstrated to have significant effects on the expression of homologous genes. Collectively, this study provides a comprehensive understanding of the genomic function of ACRs in chickpea.

Chromatin accessibility is an important feature of cis-regulatory elements that shapes gene regulation in plants; however, it has been studied less frequently in traditional medicinal plants such as Gardenia jasminoides J.Ellis (G. jasminoides). This study applied Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technology to characterize the genome-wide distribution and functional features of accessible chromatin regions (ACRs) in G. jasminoides leaves. A total of 26,461 ACRs and 13,625 associated genes were identified in this study, and our results revealed a positive correlation between the open chromatin state of ACRs and the expression levels of their associated genes. These ACRs were also found to be enriched with numerous conserved transcription factor binding motifs (TF motifs). Integration of two histone modification datasets further demonstrated that ACRs are closely associated with activating histone modifications, including H3K4me3 and H3K27ac, which work together to regulate the transcription of target genes. Additionally, luciferase (LUC) reporter assays validated the transcriptional activation activity of two candidate ACRs. Taken together, these findings elucidate the genomic features of ACRs in G. jasminoides and provide critical genomic resources for subsequent gene regulation analyses for this species.