Decoding the chromatin accessibility in Andrographis paniculata genome, a case study of genome-wide investigation of the cis-regulatory elements in medicinal plants

10.1016/j.apsb.2024.06.012

Medicinal plants have the ability to synthesize a large number of pharmaceutical metabolites, the production and regulation of which are influenced by both intrinsic signals (e.g., the spatial and temporal stage) and extrinsic environmental conditions (e.g., temperature, light availability, and water availability)1. According to the Encyclopedia of DNA Elements (ENCODE) project
, accessible chromatin regions (ACRs) served essential roles in maintaining the genome architecture and gene regulation in both mammals and plants. Nowadays, identifying ACRs within medicinal plant genomes remains a challenge, as genomic sequences have been determined for numerous species yet the characterization of such functional elements lags. In this study, we selected Andrographis paniculata (APA) as a model system to map ACRs genome-wide by the assay for transposase-accessible chromatin with sequencing (ATAC-seq) method. We aimed to uncover the genomic features of ACRs as well as their association with the expression of genes involved in secondary metabolite biosynthesis (e.g., andrographolide) within medicinal plants .