Uncovering chromatin accessibility dynamics in early maize endosperm and seed coat differentiation

The early development of maize kernels plays a crucial role in determining yield and grain quality. Deciphering chromatin accessibility dynamics can further advance our understanding of tissue-specific regulatory networks. In this study, we performed an integrated multiomics analysis to explore chromatin accessibility dynamics during cell fate transitions in early kernel development. Endosperm and seed coat samples collected at 4-10 days after pollination (DAP) are chosen for the assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) data, which reveal that chromatin accessibility undergoes stage-specific remodeling during early endosperm differentiation (4-10 DAP). Differences in distal accessible chromatin regions (dACRs) and expression patterns highlight distinct regulatory mechanisms for the zein and starch synthesis pathways, differing from recognized transcriptional co-regulation. Novel transcription factors (TF) and downstream genes were identified and validated, including DOF36, ZmNAC128, and ZmbZIP3. Notably, similar accessible chromatin regions (ACRs) patterns and expression profiles were observed for the marker genes between maternal placenta chalaza (PC) fusion zone and basal endosperm transfer layer (BETL) region of the offspring, suggesting potential co-regulatory modules. In conclusion, we generated a time-course atlas of ACRs and transcriptome to analyze specific expression regulation, construct cell differentiation trajectories, and develop cell-type-specific gene regulatory networks.