Preparation of Chromatin Fragments From Human Cells for Cryo-EM Analysis

Eukaryotic genomic DNA is packaged into chromatin, which plays a critical role in regulating gene expression by dynamically modulating its higher-order structure. While in vitro reconstitution approaches have offered valuable insights into chromatin organization, they often fail to fully capture the native structural context found within cells. To overcome this limitation, we present a protocol for isolating native chromatin fragments from human cells for cryo-electron microscopy (cryo-EM) analysis. In this method, chromatin from formaldehyde-crosslinked human HeLa S3 nuclei is digested with micrococcal nuclease (MNase) to generate mono- and poly-nucleosome fragments. These fragments are subsequently fractionated by sucrose-gradient ultracentrifugation and prepared for cryo-EM. The resulting chromatin fragments retain native-like nucleosome-nucleosome interactions, facilitating structural analyses of chromatin organization under near-physiological conditions. Key features • Chemical crosslinking preserves the native nucleosome-nucleosome interactions in chromatin fragments. • Optimal MNase digestion conditions efficiently solubilize chromatin into mono- and poly-nucleosome fragments for cryo-EM analysis. • This protocol may be adaptable to other types of cells.