Abstract
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
Highlights
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice
Our integrative analyses provide a broad overview of epigenomic landscapes, promoter chromatin features, enhancer predictions, epigenomic dynamics in different tissues, and effect of genetic variation on these rice varieties, as comprehensive rice functional DNA elements maps that lay the foundation for rice ENCODE project (The Encyclopedia of DNA Elements)
To characterize chromatin epigenomic features and identify DNA regulatory elements in rice, we first developed an enhanced chromatin immunoprecipitation method for plants that highly improved the efficiency of chromatin extraction via direct sonication of formaldehyde-fixed tissues (Fig. 1a)
Summary
Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Epigenomic information, including DNA methylation, posttranslational histone modification, and chromatin accessibility, has been characterized in rice and other plants[5] These studies provide insight into the epigenomic features of cis-regulatory elements and coordinative effects of active and inactive histone marks on transcriptional regulation[6,7,8]. Many studies have revealed the functions of genes encoding various chromatin modification factors[9,10,11] and characterized genome-wide profiles of some histone marks and DNA methylation[12,13,14,15] Despite these significant advancements, comprehensive epigenome maps across different tissues and distinct genetic backgrounds are still lacking for elucidating the dynamics of CSs and their effects on dynamic expression profiles and for assessing genetic variations affecting gene expression in plants. Our integrative analyses provide a broad overview of epigenomic landscapes, promoter chromatin features, enhancer predictions, epigenomic dynamics in different tissues, and effect of genetic variation on these rice varieties, as comprehensive rice functional DNA elements maps that lay the foundation for rice ENCODE project (The Encyclopedia of DNA Elements)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
