In plants, DNA methylation, histone modifications, and RNA interference play critically important roles in regulating chromatin structure, thereby profoundly affecting transcription and other molecular events. Recent advances in microarray and high-throughput sequencing technologies have enabled genome-wide studies of these pathways in great detail. The vast amounts of "epigenomic" data generated so far have provided new insights into the mechanisms and functions of these pathways and have broadened our understanding of the structure and organization of plant chromatin as a whole.