The papillomavirus E2 open reading frame encodes the full-length E2 protein as well as an alternatively spliced product called E8 E2C. E8 E2C has been best studied for the high-risk human papillomaviruses, where it has been shown to regulate viral genome levels and, like the full-length E2 protein, to repress transcription from the viral promoter that directs the expression of the viral E6 and E7 oncogenes. The repression function of E8 E2C is dependent on the 12-amino-acid N-terminal sequence from the E8 open reading frame (ORF). In order to understand the mechanism by which E8 E2C mediates transcriptional repression, we performed an unbiased proteomic analysis from which we identified six high-confidence candidate interacting proteins (HCIPs) for E8 E2C; the top two are NCoR1 and TBLR1. We established an interaction of E8 E2C with an NCoR1/HDAC3 complex and demonstrated that this interaction requires the wild-type E8 open reading frame. Small interfering RNA (siRNA) knockdown studies demonstrated the involvement of NCoR1/HDAC3 in the E8 E2C-dependent repression of the viral long control region (LCR) promoter. Additional genetic work confirmed that the papillomavirus E2 and E8 E2C proteins repress transcription through distinct mechanisms.Papillomaviruses (PVs) infect the squamous epithelia, inducing proliferative lesions. The PV life cycle is tightly linked with the squamous cell differentiation program. In particular, late viral gene synthesis, genome amplification, and virion production occur with the progression of epithelial cell differentiation.The PVs are small DNA viruses that contain approximately 10 open reading frames (ORFs). Like those of many viruses, PV regulatory proteins are multifunctional. The E2 ORF encodes several viral products (21). The full-length E2 protein is the most studied; it is a prototypic transcription factor, with a C-terminal DNA binding and dimerization domain, an internal hinge region, and an N-terminal "transactivation" domain (34). Initially, E2 was characterized as a transcriptional activator, and subsequently, it was shown to be a potent repressor of the long control region (LCR), which is the viral promoter that controls E6 and E7 expression (21). In addition to its transcriptional activities, E2 functions in concert with the viral E1 helicase to initiate replication of the viral DNA (21). Also, the E2 protein is involved in tethering viral genomes to the host chromatin for maintenance during mitosis (23, 50). Both the C-terminal portion of E2 (E2C), which mediates dimerization and recognition of consensus E2-binding sequences (ACCN 6 GGT) within the viral LCR, and the N terminus of E2 are required for its various transcription, replication, and genome maintenance activities (9,13,21,33,35,38,45,64).In addition to full-length E2, PVs encode an alternatively spliced product of E2 called E8 E2C. This protein contains 12 amino acids from the E8 ORF fused to the C-terminal DNA binding/dimerization domain of E2 (E2C). To date, E8 E2C transcripts have been detected for bovine ...