Identifying and assaying protein–RNA interactions is foundational to understanding the molecules’ role in both the cell and organism as a whole. Importantly, functional noncoding RNAs and their protein partners have presented RNA researchers with a new vast list of these interactions, which often do not occur through the well-described, or, canonical mechanisms, opening a floodgate of research potential for years to come. With this in mind, it is necessary to standardize assay methods, with good understanding of points of optimization. Here, we describe a simple protocol for RNA immunoprecipitation (RIP) from purified nuclei of cells. Purification of nuclei prior to RIP is important to eliminate false-positive nuclear protein–RNA interactions, especially given that specific binding to ncRNA seems to be based on cumulative electrostatic forces rather than lock-and-key binding.