d CCCTC-binding factor (CTCF) has been implicated in various aspects of viral and host chromatin organization and transcriptional control. We showed previously that CTCF binds to a cluster of three sites in the first intron of the Kaposi's sarcoma-associated herpesvirus (KSHV) multicistronic latency-associated transcript that encodes latency-associated nuclear antigen (LANA), viral cyclin (vCyclin), vFLIP, viral microRNAs, and kaposin. We show here that these CTCF binding sites regulate mRNA production, RNA polymerase II (RNAPII) programming, and nucleosome organization of the KSHV latency transcript control region. We also show that KSHV bacmids lacking these CTCF binding sites have elevated and altered ratios of spliced latency transcripts. CTCF binding site mutations altered RNAPII and RNAPII-accessory factor interactions with the latency control region. CTCF binding sites were required for the in vitro recruitment of RNAPII to the latency control region, suggesting that direct interactions between CTCF and RNAPII contribute to transcription regulation. Histone modifications in the latency control region were also altered by mutations in the CTCF binding sites. Finally, we show that CTCF binding alters the regular phasing of nucleosomes in the latency gene transcript and intron, suggesting that nucleosome positioning can be an underlying biochemical mechanism of CTCF function. We propose that RNAPII interactions and nucleosome displacement serve as a biochemical basis for programming RNAPII in the KSHV transcriptional control region. K aposi's sarcoma-associated herpesvirus (KSHV), also referred to as human herpesvirus 8 (HHV8), is a human gammaherpesvirus that infects ϳ15% of the world's population and can establish long-term latent infection in B lymphocytes of infected individuals (1-3). The virus was identified originally as the etiological agent associated with all forms of Kaposi's sarcoma (KS) (4) and was subsequently shown to be associated with pleural effusion lymphoma (PEL) and multicentric Castleman's disease (4-6; reviewed in references 2, 3, and 7). Viral pathogenesis and persistence depend on a complex balance between latent and lytic infection. In most latently infected cells, viral gene transcription is limited to a region of the viral chromosome that encodes latencyassociated nuclear antigen (LANA/ORF73), viral cyclin (vCyclin/ ORF72), vFLIP (ORF71), viral microRNAs (vmiRNAs), and kaposin (K12) (8, 9), which are critical for viral genome maintenance and host cell survival during latent infection (2, 7, 10). The latency transcripts have complex structures, with multicistronic messages and several alternative promoters, as well as lytic gene promoters for both sense and antisense orientations. Proper regulation of these various transcripts is essential for viral persistence and host cell survival.Transcriptional regulation and mRNA processing of the KSHV major latency transcripts have been investigated in some detail (8,9,(11)(12)(13)(14)(15)(16). Transcription initiation has been mapped to a s...