Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. We collected public and in-house plant epigenomic data sets and applied a Hidden Markov Model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of Arabidopsis thaliana, Oryza sativa and Zea mays, respectively. We constructed a Plant Chromatin State Database (PCSD, http://systemsbiology.cau.edu.cn/chromstates) to integrate detailed information about chromatin states, including the features and distribution of states, segments in states and related genes with segments. The self-organization mapping (SOM) results for these different chromatin signatures and UCSC Genome Browser for visualization were also integrated into the PCSD database. We further provided differential SOM maps between two epigenetic marks for chromatin state comparison and custom tools for new data analysis. The segments and related genes in SOM maps can be searched and used for motif and GO analysis, respectively. In addition, multi-species integration can be used to discover conserved features at the epigenomic level. In summary, our PCSD database integrated the identified chromatin states with epigenetic features and may be beneficial for communities to discover causal functions hidden in plant chromatin.
