Counterregulation of chromatin deacetylation and histone deacetylase occupancy at the integrated promoter of human immunodeficiency virus type 1 (HIV-1) by the HIV-1 repressor YY1 and HIV-1 activator Tat.

Biochemical and epigenetic studies have revealed that nucleosomes at eukaryotic promoters function as dynamic units in transcriptional regulation (4, 5, 8, 18, 21, 38, 45). The nucleosome core contains a central histone octamer consisting of four histone dimers, H2A, H2B, H3, and H4 (30). Posttranscriptional modifications of the tails (31, 42) of histone proteins, such as acetylation (19, 48, 50), methylation (43), and ubiquination and phosphorylation (9, 11), modulate the conformation of a nucleosome. Nucleosome structure is thought to influence the accessibility of transcription factors to the promoter and the formation of the transcription initiation complex. Hyperacetylation of core histones is correlated with transcription activation (7, 20, 35) while hypoacetylation is correlated with repression (27, 32). Acetylation is reversed by histone deacetylases (HDACs), a family of enzymes that removes acetyl groups from the tails of acetylated core histones (14, 22, 49). Although the mechanism by which HDACs regulate nucleosome structure is not clear, several transcriptional repressors associate with HDACs. Interestingly, DNA-binding domains of HDACs have not yet been identified. Targeted recruitment of HDACs to a specific promoter by sequence specific DNA-binding factors is a favored model to explain the selective silencing of individual eukaryotic genes (23, 24, 33, 36, 37). Human immunodeficiency virus type 1 (HIV-1) is an intracellular parasite dependent on the host cellular metabolism to complete its life cycle. Once integrated into the host genome, the 5′ long terminal repeat (LTR) of HIV-1 serves as the promoter regulating viral gene expression and replication. HIV-1 can establish a quiescent, latent state within resting CD4+ T cells (16). Mechanisms that allow the establishment or maintenance of proviral quiescence have not yet been elucidated. While recruitment of selected host transcription activators and viral activator Tat to the LTR allows powerful activation of HIV transcription and viral replication, restriction of LTR expression by host repressors may allow activated, infected lymphocytes to return to the nonproductive resting state and establish viral quiescence. A positioned nucleosome (nuc 1) spanning the region from +1 to +155 with respect to the transcription start site of HIV-1 LTR has been mapped in DNase I protection studies (52, 53). Experiments examining the accessibility of integrated HIV-1 LTR to restriction endonucleases at this region suggest that disruption of this nucleosome accompanies transcriptional activation of integrated LTR by the viral factor Tat (13, 40) or the HDAC inhibitors trichostatin A (TSA) and trapoxin (51). Our previous studies have identified two ubiquitous transcription factors, YY1 and LSF, that cooperate in the repression of HIV-1 LTR and viral production (12, 34, 44). LSF binds to a sequence located at the region from −10 to +27 of the HIV-1 LTR and recruits YY1 to LTR via a specific interaction with the zinc-finger domain of YY1. YY1 and LSF repress the LTR via recruitment of HDAC1. These three cellular factors copurify in a complex binding the LTR RCS site, and repression of HIV LTR expression requires both LSF capable of binding the LTR RCS site and YY1 capable of recruitment of HDAC1 (12). Further, mutations within the RCS ablate the inhibitory effect of YY1 (44), TSA blocks YY1-mediated repression (12), and sequence-specific polyamides antagonizing LSF binding to LTR allow HIV expression in vivo (J. J. Coull et al., unpublished data). Deacetylation of histones may remodel nuc 1 at LTR, resulting in transcriptional repression of HIV-1. We have analyzed in vivo factor occupancy at the nuc 1 region of the integrated LTR by using a chromatin immunoprecipitation (ChIP) assay. We demonstrate for the first time that ChIP assays detect HDAC1 at the nuc 1 site of the LTR and loss of HDAC1 after TSA treatment in vivo. We then examined the occupancy of HDAC1 and the acetylation state of nuc 1 simultaneously and found an inverse correlation between LTR expression and both HDAC1 occupancy and nuc 1 hypoacetylation. Further, we found that the HIV-1 activator Tat decreased HDAC1 occupancy, while the LTR host repressor YY1 could overcome this effect, decreasing H4 acetylation at nuc 1 and increasing HDAC1 occupancy.