Genome‐wide DNase I‐hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane

Abstract

SUMMARYThe characterization of cis‐regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome‐wide identification of DNase I‐hypersensitive sites (DHSs) in leaf and stem tissues of the auto‐octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf‐ and stem‐dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue‐specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene‐responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue‐specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.

Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

“…In sugarcane, more than 16,000 genes have been identified as potential targets regulated by ERF109, indicating that ERF109 has a broad influence on gene expression. Functions are diverse and include metabolic activities such as Rubisco activity, triggering hormone biosynthesis such as that of cytokinins, and gibberellin-mediated responses (Yu et al, 2024). ERF109 was not expressed in the internodes of any of the analyzed sugar-accumulating plants or in the younger internodes of S. spontaneum , but there was significant expression in its older internodes.…”