Conjugation of the polypeptide ubiquitin (Ub) to numerous substrate proteins impacts and regulates virtually all cellular processes. Eight distinct Ub polymer linkages specifying different functional outcomes are generated in cells, yet the roles of some atypical poly-Ub topologies, in particular K27-linked Ub chains, remain poorly understood due to a lack of tools for specific detection of these low-abundant linkages. Here, we utilized a Ub replacement strategy enabling chemically inducible disruption of individual Ub linkage types to demonstrate that K27-linked Ub chains are essential for proliferation and viability of human cells. We show that K27 linkages are predominantly a nuclear modification and that disabling their formation deregulates cell cycle progression and responses to DNA damage in a manner that is epistatic with inactivation of the ATPase p97. Consistently, targeted ablation of K27-linked Ub chain generation alters the functional status of nuclear p97 complexes and impairs p97 activity. Our findings establish a critical role of K27-linked ubiquitylation in supporting cell proliferation and implicate this enigmatic Ub modification in p97-dependent processing of ubiquitylated client proteins in the nucleus.