Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants

The precise positioning of nucleosomes along the underlying DNA is critical for a variety of biological processes, especially in regulating transcription. The interplay between nucleosomes and transcription factors for accessing the underlying DNA sequences is one of the key determinants that affect transcriptional regulation. Moreover, nucleosomes with various packing statuses confer distinct functions in regulating gene expressions in response to various internal or external signals. Therefore, global mapping of nucleosome positions is one informative way to elucidate the relationship between patterns of nucleosome positioning/occupancy and transcriptional regulations. MNase digestion coupled with high-throughput sequencing (MNase-seq) has been utilized widely for global mapping of nucleosome positioning in eukaryotes that have a sequenced genome. We have developed a robust MNase-seq procedure in plants. It mainly includes plant nuclei isolation, treatment of purified nuclei with MNase, gel recovery of MNase-trimmed mononucleosomal DNA with an approximate size of 150 bp, MNase-seq library preparation followed by Illumina sequencing, and data analysis. MNase-seq has already been successfully applied to identify genome-wide nucleosome positioning in model plants, rice, and Arabidopsis thaliana.