Altered chromatin accessibility in light and hormone responses of rice seedlings

Light is essential for plant adaptation and the survival of photoautotrophs. However, our understanding of how rice (Oryza sativa) seedlings transition from skotomorphogenesis to photomorphogenesis remains limited, especially at the epigenetic level. Here, we show that light greatly alters chromatin accessibility during the switch from skotomorphogenesis to photomorphogenesis. Photosynthesis-related genes exhibited more open chromatin, although more closed chromatin was identified after light exposure at the genome-wide scale. These largely closed chromatin structures parallel the reduced transcriptional activity revealed by RNA polymerase II (Pol II) occupancy. Moreover, transcription activators of GOLDEN2-LIKE (GLKs), which control chloroplast biogenesis and development, primarily bind to light-induced open chromatin regions, thereby functionally establishing rice as a photoautotroph. Additionally, the integrated analysis of chromatin accessibility and Pol II occupancy in response to exogenous indole-3-acetic acid (IAA) and abscisic acid (ABA) application revealed that IAA and ABA have active and repressive roles in inducing chromatin openness and transcriptional activity in rice seedlings, respectively. Collectively, our results provide insight into the epigenomic regulation of rice seedling photomorphogenesis and valuable resources for studying the roles of cis-regulatory elements in the regulation of hormone responses, specifically IAA and ABA, in rice seedlings.