While previous studies have shown that histone modifications could influence 
plant growth and development by regulating gene transcription, knowledge about 
the relationships between these modifications and gene expression is still 
limited. This study used chromatin immunoprecipitation followed by 
high-throughput sequencing (ChIP-Seq), to investigate the genome-wide 
distribution of four histone modifications: di and trimethylation of H3K4 
(H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in 
Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study 
explored DNase-Hypersensitive (DH) sites along the rice genome. The histone 
marks appeared mainly in generic regions and were enriched around the 
transcription start sites (TSSs) of genes. This analysis demonstrated that the 
four histone modifications and the DH sites were all associated with active 
transcription. Furthermore, the four histone modifications were highly 
concurrent with transcript regions-a promising feature that was used to predict 
missing genes in the rice gene annotation. The predictions were further 
validated by experimentally confirming the transcription of two predicted 
missing genes. Moreover, a sequence motif analysis was constructed in order to 
identify the DH sites and many putative transcription factor binding sites.