Protocol for visualization of ultrafine nuclear structures in cultured cells using protein retention expansion microscopy

In the nucleus, multivalent interactions between DNA, RNA, and proteins form functional networks that drive nuclear metabolism, such as transcription and RNA processing. Here, we present a protocol to visualize the subnuclear distribution of nuclear proteins in cultured cells using protein retention expansion microscopy (proExM). We describe steps for immunostaining, sample expansion, sample bonding on glass coverslips, and imaging with confocal microscopy. This protocol is a reproducible and cost-effective procedure for studying ultrafine nuclear organizations. For complete details on the use and execution of this protocol, please refer to Masuda et al.¹.