Construction Of Rice Epigenomic Map And Database

Epigenetic modification featured in the gene regulation without changing the sequence characteristics.Rice is an important and the most studied gramineous plant in the field of genomics,in addition to the extensively studied model plants such as arabidopsis and maize.However the comprehensive multi-tissues and multi-varieties reference epigenomes remain unexplored in rice.In this study,we analysised chromatin accessibility,DNA methylation,transcriptome,five histone modifications and RNA polymerase II occupancy epigenomic data across various tissues(young leaves,mature leaves,panicles and roots)in 20 cultivars.By integrating such a large of datasets we construct comprehensive epigenome landscapes in whole genome field.Approximately 81.8% of rice genomes are annotated with different epigenomic properties.Then we collected the public epigenome data of rice and constructed the comprehensive rice epigenome database Rice ENCODE,which is the largest one for rice epigenomics up to our best knowledge.The highlights of this study are as follows:1.Refinement of 4300 promoter regions used open chromatin and H3K4me3-marked regions.2.We verified the accuracy of the newly discovered bivalent state of coexistence of H3K9me2-H3K4me1 through Ch IP-re Ch IP data.We not only found this state is enriched in Copia-like transposons and most of them exist in long intron regions but also exploring the relationship between gene and state in expression level.3.We identified 3895 enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions.4.We observed that active and repressive histone modifications and the predicted enhancers vary largely across tissues,whereas inactive chromatin states are relatively stable.When comparing among varieties,the active histone modification is relatively stable,but the heterochromatin region is obviously different,which is probably related to the genetic variation.5.By comparing epigenomic signals,We identified a large number of different regions between Xian/Indica and Geng/Japonica,and all of them fell on the core regulatory regions.They are probably potential functional differences regions,which is likely lead to the phenotypic difference between Xian/Indica and Geng/Japonica.6.In this study,we constructed a comprehensive rice Encyclopedia of DNA Elements database(Rice ENCODE),which can help us outline the rice epigenome comprehensively,and offered an important platform for studying rice molecular breeding,subgroup comparison and differences in epigenetic regulation.In summary,the construction of the epigenome map annotates the functional elements in the rice genome,and analyzes the change trend about epigenome signal in multiple tissues and multiple varieties.The rice epigenome database provides a platform for rice researchers to study these epigenome data.These studies constitute a valuable resource and tools for functional element annotation in rice and indicate the central role of epigenomic information in transcriptional regulation.