Different histone families in intracellular SV40 nucleoprotein complexes with respect to the acetylation turnover

Programmed remodeling of hyperacetylated histone H4 and H3 organization on the SV40 genome during lytic infection

The presence of nucleosomes containing hyperacetylated histone H4 and H3 on the early, late, and promoter regions of the SV40 genome in chromosomes isolated 30 min, 8 h, and 48 h post-infection was determined by chromatin immunoprecipitation (ChIP) analysis with PCR amplification of fragmented SV40 chromatin using two complementary strategies. In chromosomes isolated at 30 min post-infection hyperacetylated H4 was found intermittently in all the three regions with no preference for one region over the other. In contrast, hyperacetylated H3 was organized primarily within the promoter region and occasionally elsewhere. At 8 h post-infection, nucleosomes with both hyperacetylated H4 and H3 were found regularly associated with all three regions of the SV40 genome. Finally, in SV40, chromosomes isolated 48 h post-infection hyperacetylated H4 and H3 were found frequently associated with all regions of the chromosome although hyperacetylated H4 was preferentially associated with the late region. The changing patterns of organization of hyperacetylated histones in SV40 chromosomes during the course of a lytic infection presumably reflects the different biological functions of the SV40 chromatin at each of the time points.

Hyperacetylation and differential deacetylation of histones H4 and H3 define two distinct classes of acetylated SV40 chromosomes early in infection

SV40 chromosomes undergoing encapsidation late in infection and SV40 chromatin in virions are hyperacetylated on histones H4 and H3. However, the fate of the SV40 chromosomes containing hyperacetylated histones in a subsequent round of infection has not been determined. In order to determine if SV40 chromosomes undergo changes in the extent of histone acetylation during early infection, we have analyzed SV40 chromosomes isolated 30 min and 3 h postinfection by quantitative ChIP assays, depletion ChIP assays, competitive ChIP assays, and ChIP assays combined with restriction endonuclease sensitivity using antibodies to hyperacetylated histones H4 and H3. We have shown that at 30 min postinfection, the hyperacetylated histones are associated with two distinct classes of SV40 chromosomes. One form is hyperacetylated specifically on histone H4 while a second form is hyperacetylated on both H4 and H3. Both forms of chromosomes appear to contain a nucleosome-free promoter region. Over the course of the next few hours of infection, the class of SV40 chromosomes hyperacetylated on only H4 is reduced or completely eliminated through deacetylation.

SP1 and AP-1 elements direct chromatin remodeling in SV40 chromosomes during the first 6 hours of infection

To identify the SV40 regulatory sequences responsible for the chromatin remodeling associated with early transcription, SV40 chromosomes containing potential remodeling sequences inserted adjacent to a reporter region were isolated at various times within the first 6 h of infection and analyzed by a combination of restriction endonuclease digestion and competitive PCR amplification. The sequences analyzed included the early domain, the enhancer, the late domain, the early phasing element, the AP-1 element, two tandem copies of the SP1 element, and the AP-4 element. From 30 min to 3 h postinfection only the enhancer, the AP-1 element, and the two tandem copies of the SP1 element caused a change in nuclease sensitivity consistent with chromatin remodeling. These results suggest that the changes in chromatin structure seen in the promoter during activation of early transcription are most likely a result of remodeling by the AP-1 and/or SP1.

Identification and protein analysis of polyomavirus assembly intermediates from infected primary mouse embryo cells

A method is described for the isolation of polyoma virus assembly intermediates from infected mouse embryo cells. Sucrose gradient profiles revealed the presence of 90 S, 200 S, and 240 S intermediates. These intermediates were shown to be sensitive to a number of factors: ionic condition of the isolation buffer, presence of chelating agents and nonionic detergents during isolation, and sonication of nuclei during extraction of intermediates. Pulse-chase experiments demonstrated that the order of formation of the intermediates to be 90 S----240 S, with the 200 S particles as a possible intermediate form linking the 90 S and 240 S particles. Viral structural proteins VP1, VP2, and VP3 were shown to be present on all three intermediates, but the ratio of each protein varied on each intermediate species. Two-dimensional gel electrophoresis demonstrated that the distribution of the VP1 isoelectric focusing species were different among the three intermediates. Histone H1 was found exclusively with the 90 S species.

A comparison of methods for the extraction of nucleoprotein complexes from SV40-infected cells

A comparison was made between two alternative methods for the nuclear extraction of Simian virus 40 (SV40) virions and nucleoprotein complexes (NPCs) from SV40-infected TC7 cells. The low-salt hypotonic method of Su and DePamphilis (1976) was compared with the detergent method of Garber et al. (1978), since other methods had been shown to result in virion breakdown. There was no disruption of mature SV40 virions with either of these extraction procedures. There was, however, considerably more effective extraction of SV40 NPCs, known to contain large tumor (T) antigen, using the low-salt hypotonic method as opposed to the detergent method. Thus, the low-salt hypotonic method for extraction should be the method of choice when studying SV40 DNA replication or the function of SV40 T antigen in SV40 nucleoprotein complexes.

Generation of capsids from unstable polyoma virions

Polyomavirus was purified from infected mouse cell lysates under mild physiological conditions. When analyzed in a sucrose gradient, a major virus peak (240S) was identified. This sucrose-isolated virus could be divided into two populations based on its stability to CsCl gradient centrifugation. Members of the unstable population were shown to eject their DNA cores when subjected to CsCl gradient centrifugation, forming empty capsids, whereas the stable population was unaffected by the same CsCl treatment. Formaldehyde fixation of the 240S virus particles stabilized the virions and prevented ejection of DNA and generation of empty capsids. When formaldehyde-fixed 240S virus was examined with the electron microscope, only full virions were observed. These results indicate that polyoma capsids are not preformed in vivo, but instead are generated when infected cell lysates are subjected to harsh CsCl purification procedures.

Alteration in the simian virus 40 maturation pathway after butyrate-induced hyperacetylation of histones

The role of histone acetylation in the replication and maturation pathways of simian virus 40 was assessed. Histones were hyperacetylated by briefly exposing infected cells to sodium butyrate. Viral DNA in cells exposed to butyrate was found to reenter replication to a greater extent and mature to the previrion form to a lesser extent than viral DNA in control cells. Previrions formed in the presence of butyrate had altered sedimentation properties. These data suggest that increased acetylation of histones is not the signal for removal of DNA from the pool of molecules available for replication. It appears, in fact, that hyperacetylation retards entry into and progression along the maturation pathway.