Vol.:(0123456789) 1 3 Theoretical and Applied Genetics https://doi.org/10.1007/s00122-019-03518-7 REVIEW Understanding epigenomics based on the rice model Yue Lu 1  · Dao‑Xiu Zhou 1,2  · Yu Zhao 1 Received: 27 August 2019 / Accepted: 18 December 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2020 Abstract Key message The purpose of this paper provides a comprehensive overview of the recent researches on rice epig- enomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Abstract Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profling and three-dimensional chromatin structure studies reveal specifc features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chro- matin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, ftness, and yield. In this review, we summarize and analyze recent advances in rice epigenom- ics and discuss challenges and directions for future research in the feld. Introduction Epigenome refers to the comprehensive collection of genome-wide epigenetic phenomena, including DNA meth- ylation patterns, histone modifcations, and chromatin struc- ture under specifc environmental conditions or in distinct cell types. Thus, the epigenome difers between cell types and contributes to cell-type-specifc gene expression by organizing the chromatin structure, exposing or enclosing active cis-regulatory elements, or through posttranscrip- tional activities. Therefore, the epigenome is pivotal to plant development, biomass, and stress responses. Recently, epig- enomic maps have been established in many crops, such as rice, maize, wheat, cotton, tomato, and soybean (Cantu et al. 2010; Davis-Richardson et al. 2016; Li et al. 2008; Wang et al. 2016, 2009; Zhong et al. 2013a). Because of its small genome, easily genetic manipulation, extensive collinearity with other cereal crops such as maize, wheat, and barley, highly efcient and mature genetic transformation system, rich germplasm resources, a long history of research, and the frst cereal crop genome to be sequenced, rice has become a model organism for crop epigenome research (https://rice. plantbiology.msu.edu). In this review, we focus particularly on profles and functions of rice DNA methylation, histone modifcations, noncoding RNAs and three-dimensional (3D) genome structure and emphasize the use of epigenomic information to delineate rice gene regulatory sequences and developmental programs. We also discuss perspectives on the progress of the epigenomics feld and challenges ahead. DNA methylation DNA methylation landscape and dynamics DNA methylation is an important epigenetic mark, which includes 5-methylcytosine (5mC), 6-methyladenine (6mA), 4-methylcytosine (4mC), and 7-methylguanine (7mG). Among them, 5mC is the frst identifed DNA methylation and known as the “ffth base” of DNA (Ehrlich and Wang 1981). DNA 5mC, which occurs at CG, CHG, and CHH (where H = A, C, or T) sequences in plants, is a hallmark of the repression of repetitive sequences and transposable elements (TEs) (Law and Jacobsen 2010). It is proposed that DNA methylation is more important in crops that have Communicated by Qifa Zhang. * Yu Zhao zhaoyu@mail.hzau.edu.cn 1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China 2 Institute of Plant Science of Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University Paris-Saclay, 91405 Orsay, France