Identification of nuclear matrix proteins tightly bound to soluble simian virus 40 chromosomes

Differential regulation by SV40 T-antigen binding at site I defines two distinct classes of nucleosome-free promoter

BACKGROUND

T-antigen binding site I has been shown previously to play a role in regulating the proportion of Simian Virus 40 (SV40) chromosomes containing a nuclease hypersensitive promoter region. In order to determine whether these changes in nuclease hypersensitivity were a result of changes in the proportion of SV40 chromosomes, which contained a nucleosome-free promoter region, SV40 chromosomes were visualized by electron microscopy.

METHODS

SV40 chromosomes were prepared from cells infected with either wild-type or mutant virus lacking T-antigen binding site I, and the chromosomes were analyzed by electron microscopy for the presence of nucleosome-free regions.

RESULTS

Both the wild-type and mutant chromatin were found to contain heterogeneous nucleosome-free promoter regions consisting of small (3-4 times the normal internucleosomal distance) and large (greater than four times the normal internucleosomal distance) regions. Quantification of the proportion of chromosomes containing each type of region indicated that deletion of site I resulted in a 25% increase in the proportion of chromosomes containing a large nucleosome-free region but had no effect on the proportion of chromosomes containing a small nucleosome-free region.

CONCLUSIONS

The results indicate that there are two distinct classes of nucleosome-free promoter region in SV40 chromatin and that T-antigen binding to site I is specifically involved in the regulation of only the class that contains a large nucleosome-free region.

Generation of a nucleosome-free promoter region in SV40 does not require T-antigen binding to site I

The relationship between T-antigen interactions at Site I and the presence of a nucleosome-free promoter in SV40 chromatin was examined by analyzing chromatin from mutants defective for T-antigen interaction at site I (cs 1085, scs111, and tsA58) and their parental wild-type strains (776, SVS, and VA45-54, respectively). As judged by sensitivity to digestion with restriction endonucleases that recognize unique sequences within the promoter region (BglI, KpnI, and MspI), a nucleosome-free promoter was observed in a substantially larger proportion of chromosomes from the defective mutants than their wild-type parents. This result demonstrates that T-antigen binding to site I is not necessary for setting the early boundary of the nucleosome-free region, although it may function directly or indirectly in determining the proportion of chromosomes containing this feature.

Analysis of the origin-specific nucleosome-free region in SV40 encapsidation intermediates

The presence of a nucleosome-free region at the replication origin in encapsidation intermediates of SV40 was determined by measuring the sensitivity of the intermediates to digestion by restriction endonucleases which lie within (BglI and SphI) or outside of this region (KpnI, MspI, and EcoRI). As judged by hypersensitivity to digestion with BglI and SphI, the origin-specific nucleosome-free region was found to be present in nonencapsidated and partially encapsidated SV40 chromosomes and previrions, but not virions.

Synthesis and stability of nuclear matrix proteins in resting and serum-stimulated Swiss 3T3 cells

The major [35S]methionine-radiolabeled nuclear matrix proteins of mouse 3T3 cells were isolated, and most of these were found to be similar in molecular weight, charge, and protease fingerprint to the nuclear matrix proteins of African green monkey kidney cells, which are found tightly bound to simian virus 40 chromosomes. These nuclear matrix proteins were found to be synthesized in quiescent and serum-stimulated cells and to be turned over slowly during pulse-chase experiments. In contrast, a 70-Kd (kilodalton) neutral protein identified as lamin a was found to be turned over rapidly, producing a 68-Kd protein with a similar isoelectric point. In addition, we observed a decrease in the amounts of two chromatin-bound matrix proteins and a relative increase in lamin a following labeling in the presence of 2 micrograms/ml actinomycin D. However, these effects do not appear to be a result of inhibition of transcription, since they were not observed with other inhibitors (alpha-amanitin and 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole).