Characterization of Plant 3D Chromatin Architecture, In Situ Hi-C Library Preparation, and Data Analysis.

In the mammalian nucleus, 3D organization of the chromatin plays an important role in the regulation of gene expression. Similar chromatin structures such as A/B compartments, domains, and loops have now been found in plants, yet their biological function remained to be further elucidated. In this chapter, we present a detailed protocol for examining genome-wide chromatin interaction using in situ Hi-C optimized for plant tissues. We also provide a step-by-step bioinformatic workflow for Hi-C sequencing data alignment, and subsequent compartment, domain, and chromatin loop identification.