Abstract
Advancement of high-throughput sequencing technology has provided novel discoveries in plant science. Especially, "Epigenomics" is a novel noteworthy research area using this technology and has contributed greatly to further our understanding of epigenetic mechanisms, such as histone modifications and DNA methylations, involved in many biological phenomena in eukaryotes. Alterations of histone modifications and DNA methylation correlate with regulation of gene activity and genome maintenance. The sample preparation and computational analysis are the critical steps for precise identification of the epigenome information using the high-throughput sequencers. The quality of the histone modification data that are obtained by the high-throughput sequencing technology depends on the methods of Chromatin Immunoprecipitation (ChIP) and computational analysis. In this technical note, we refer to the the practical problems in the epigenome analysis and describe the methods that we have optimized for Arabidopsis ChIP analyses to identify site-specific and genome-wide histone modification status.
