Oryza sativa Transcriptome or Gene expression. Oryza sativa

Reference epigenomic annotation is instrumental for understanding transcriptional regulation and other cellular activities, but comprehensive epigenomic maps of rice (Oryza sativa) are lacking. Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues in three rice varieties (Minghui63, Zhenshan97 and Nipponbare). Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.