The life cycle of human papillomaviruses (HPVs) is tightly linked to the differentiation program of the host's stratified epithelia that it infects. E1∧ E4 is a viral protein that has been ascribed multiple biochemical properties of potential biological relevance to the viral life cycle. To identify the role(s) of the viral E1 ∧ E4 protein in the HPV life cycle, we characterized the properties of HPV type 16 (HPV16) genomes harboring mutations in the E4 gene in NIKS cells, a spontaneously immortalized keratinocyte cell line that when grown in organotypic raft cultures supports the HPV life cycle. We learned that E1 ∧ E4 contributes to the replication of the viral plasmid genome as a nuclear plasmid in basal cells, in which we also found E1 ∧ E4 protein to be expressed at low levels. In the suprabasal compartment of organotypic raft cultures harboring E1 ∧ E4 mutant HPV16 genomes there were alterations in the frequency of suprabasal cells supporting DNA synthesis, the levels of viral DNA amplification, and the degree to which the virus perturbs differentiation. Interestingly, the comparison of the phenotypes of various mutations in E4 indicated that the E1 ∧ E4 protein-encoding requirements for these various processes differed. These data support the hypothesis that E1 ∧ E4 is a multifunctional protein and that the different properties of E1 ∧ E4 contribute to different processes in both the early and late stages of the virus life cycle.Human papillomaviruses (HPVs) are small, doublestranded DNA viruses that infect the stratified epithelium lining the skin, anogenital tract, and oral cavity. Viral infection generally causes hyperproliferative lesions such as warts and condyloma. High-risk, mucosotropic (previously termed anogenital) HPVs, most commonly HPV type 16 (HPV16), are also associated with malignant tumors of the anogenital tract and oral cavity and are now accepted as the major causative agent of cervical cancer (64, 69). The life cycle of HPVs is tightly linked to the differentiation program of the host epithelium. HPVs infect basal keratinocytes, presumably at a site of wounding, and they establish their double-stranded, circular DNA genome as an extrachromosomal nuclear plasmid (replicon) at a low copy number. In these proliferating basal cells, early viral genes are selectively expressed, and viral DNA replication occurs along with cellular chromosomal DNA replication to maintain viral DNA copy numbers in both parent and daughter cells. This stage of the viral life cycle within basal cells is called the nonproductive or early stage because no new virus is made. As the infected cells migrate upward and undergo terminal differentiation, the productive or late stage of the viral life cycle begins. In the suprabasal compartment of the epithelium, the viral DNA is amplified, and this is followed by the expression of the late viral genes, including those encoding the structural proteins that form the capsid. Viral DNA is packaged into these capsids to form progeny virions that accumulate in the most superf...