Here we show that the 5 end and the middle region of the L2 coding sequence of human papillomavirus type 16 contain strong inhibitory RNA sequences termed inhibitory regions I and II. This is in contrast to L1, which contains one inhibitory region in the 5 end of the coding region. Inhibitory regions I and II acted in cis to reduce L2 mRNA levels and to inhibit the use of the mRNA. In tandem, the two regions reduced L2 mRNA production to undetectable levels. Specific mutational inactivation of the two inhibitory elements in the 5 end and in the middle region of L2 by the introduction of nucleotide substitutions that changed the nucleotide sequence but not the protein sequence resulted in production of high levels of L2 mRNA and protein. In contrast to L2, a partial L1 mutant in which only the first one third of L1 was mutated produced levels of L1 mRNA and protein similar to those in a full L1 mutant. In addition, the constitutive transport element of simian retrovirus type 1 overcomes the effect of the inhibitory sequences of L1 but not L2.Human papillomaviruses (HPVs) are a group of small, double-stranded DNA tumor viruses (27). The HPV genome is approximately 8 kb in length and can be divided into an early (E) and late (L) region ( Fig. 1) (16). The late region codes for the two structural proteins L1 and L2, which are the major and minor capsid proteins, respectively. Together they form the icosahedral capsid that contains the viral genomic DNA.The HPV life cycle is tightly linked to the differentiation stage of the infected cell (16). Upon entry into the basal epithelial cells, only early genes are expressed. As the cell progresses towards terminal differentiation, induction of viral DNA replication occurs to high levels (30). This is followed by activation of viral late gene expression and assembly of infectious viral particles at the uppermost layers of the epithelium. The requirement for terminal cell differentiation has hampered the study of the viral life cycle in vitro. However, propagation of papillomavirus has been successful in a xenograft model and in the organotypic (raft) culture systems that induce terminal cell differentiation (10,21,29). Propagation of HPVcontaining cell lines in these systems leads to the completion of the differentiation-dependent life cycle of HPVs in vitro. The L1 and L2 proteins were detected only after culturing of the HPV DNA-containing cells in raft cultures and then only in the superficial layers of the terminally differentiated cells (12-14, 21-23). L1 and L2 proteins were not seen in the proliferating keratinocytes, demonstrating that expression of L1 and L2 is efficiently suppressed in proliferating cells.We are interested in the regulation of HPV late gene expression, and we and others have identified inhibitory sequences on late HPV mRNAs (1, 24-26). These sequences are located in the late 3Ј untranslated region (6,15,17,18,33) and in the L1 and L2 coding regions (4,5,28,31). Our previous work on HPV-16 L1 expression demonstrated the presence of cis-acting negat...