Genome-Wide Identification of Chromatin Domains Anchored at the Nuclear Periphery in Plants

As a functional compartment, the nuclear periphery plays critical roles in regulating the spatial organization of chromatin in the nuclei and gene expression. Generally, the nuclear periphery is a transcriptionally repressed compartment enriched for silenced chromatin. Methods of investigating chromatin positioning at the nuclear periphery in plants will substantially advance our understanding of transcriptional regulation in this subnuclear compartment. Here, we describe a detailed RE-ChIP-seq (restriction enzyme-mediated ChIP-sequencing) protocol, which combines restriction enzyme-mediated chromatin fragmentation, chromatin immunoprecipitation, and next generation sequencing approaches, to identify chromatin that positioned at the nuclear periphery in Arabidopsis. Different from a regular chromatin immunoprecipitation method, RE-ChIP allows specific enrichment of chromatin located near the protein of interest regardless of having direct interactions. In principle, this approach is applicable to identify target chromatin of transcriptional coregulators, which often do not directly bind DNA.