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LANA is essential for tethering the KSHV genome to metaphase chromosomes and for modulating host-cell gene expression, but the binding sites in the host-chromosome remain unknown. Here, we use LANA-specific chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to identify LANA binding sites in the viral and host-cell genomes of a latently infected pleural effusion lymphoma cell line BCBL1. LANA bound with high occupancy to the KSHV genome terminal repeats (TR), and to a few minor binding sites within the latency control region encoding that LANA transcript. We identified 256 LANA binding peaks with p < 0.01 and overlap in two independent ChIP-Seq experiments. We validated several of the high-occupancy binding sites by conventional ChIP assays and quantitative PCR. Two candidate DNA sequence motifs were identified, and confirmed to bind purified LANA protein, although with weaker affinity compared to viral TR binding site. More than half of the LANA binding sites (170/256) could be mapped to within 2.5 kb of a cellular gene transcript. Pathways and Gene Ontogeny (GO) analysis revealed that LANA binds to genes within the p53 and TNF regulatory network. Further analysis revealed partial overlap of LANA binding sites with STAT1 binding sites in several interferon (IFN)-g regulated genes. We show that ectopic expression of LANA can down-modulate IFN-g mediated activation of a subset of genes, including the TAP1 peptide transporter and proteasome subunit beta type 9 (PSMB9) required for class I antigen presentation. Our data provides a potential mechanism through which LANA may regulate several host cell pathways by direct binding to gene regulatory elements. Study of KSHV LANA

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