The 3D folding of the genome is linked to essential nuclear processes including gene
expression, DNA repair, and replication. Chromatin conformation capture assays such
as Hi-C are providing unprecedented insights into higher-order chromatin structure.
Bulk Hi-C of millions of cells enables detection of average chromatin features at
high resolution but is challenging to apply to rare cell types. This chapter describes
our recently developed single-nucleus Hi-C (snHi-C) approach for detection of chromatin
contacts in single nuclei of murine oocytes and one-cell embryos (zygotes). The step-by-step
protocol includes isolation of these cells, extraction of nuclei, fixation, restriction
digestion, ligation, and whole genome amplification. Contacts obtained by snHi-C allow
detection of chromatin features including loops, topologically associating domains,
and compartments when averaged over the genome. The combination of snHi-C with other
single-cell techniques in these and other rare cell types will likely provide a comprehensive
picture of how chromatin architecture shapes cell identity.