Role of CTCF in HPV replication and viral DNA looping

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 DESCRIPTION (provided by applicant): Human papillomaviruses (HPV) are the causative agents of cervical, anal and many oral cancers. While prophylactic vaccines to prevent HPV infections have been developed, there is no effective treatment for existing HPV lesions. It is therefore of critical importance to understand how the productive life cycle of high-risk HPVs is regulated to identify potential new therapeutic targets. HPVs infect stratified squamous epithelia and link their productive life cycles to the differentiation of the infected cell. Vegetative genom replication, late gene expression, and virion assembly are restricted to the nuclei of highly differentiated cells present in the uppermost epithelial layers. When HPV infected cells migrate from the basal layer, they become arrested in G1 and are induced to re-enter S/G2 phases in the most differentiated layers to allow for vegetative viral DNA replication in a process referred to as amplification. My laboratory recently demonstrated that the cohesin protein, SMC1 and the insulator transcription factor, CTCF, as critical regulators of the HPV life cycle. The cohesin protein, SMC1, is necessary for sister chromatid association prior to mitosis. In addition the phosphorylated form of SMC1 plays a critical role in the NBS1/BRCA1 dependent arm of the ATM response. In HPV positive cells SMC1 is constitutively phosphorylated and localized to distinct nuclear foci in complexes with γ-H2AX, as well as CHK2 and are bound to HPV DNA. Importantly, knockdown of SMC1 blocks differentiation-dependent genome amplification. pSMC1 also forms complexes with the insulator transcription factor CTCF and our studies show that it binds to conserved sequence motifs in the L2 late region of HPV 31. Similar motifs are found in most HPV types. Knockdown of CTCF with shRNAs blocks genome amplification and mutation of the CTCF binding motifs in the L2 ORF inhibits stable maintenance of viral episomes in undifferentiated cells as well as amplification of genomes upon differentiation. These findings suggest a model in which SMC1 factors are constitutively activated in HPV positive cells and recruited to viral genomes through complex formation with CTCF that regulate viral replication. CTCF complexes mediate insulator function by blocking adjacent enhancer function and CTCF complexes bound to HPV genomes also act as insulator elements that shield cryptic viral promoters from activation by the HPV enhancer element in the URR. CTCF acts to organize chromatin loops that regulate transcription, splicing, replication and recombination. This application focuses on understanding the role of CTCF in mediating stable maintenance of HPV episomes in undifferentiated cells, chromatin organization of viral DNAs and the inter- as well as intramolecular looping of viral DNAs. This is a new area of study for human papillomaviruses that I believe will help us understand the role of supramolecular structures of viral DNAs in the viral life cycle. Aim 1: What is the role of CTCF sites in HPV replication and gene expression? Aim 2: Does HPV form inter or intramolecular DNA loops through CTCF interactions?