T-antigen is the only detectable protein on the nucleosome-free origin region of isolated simian virus 40 minichromosomes

T-antigen is not bound to the replication origin of the simian virus 40 late transcription complex

Simian virus 40 tumor antigen (T-antigen) plays a central role in determining which gene is transcribed from viral DNA late in infection. Results from several studies have led to a model in which the binding of T-antigen to the viral origin of replication results in repression of transcription from the stronger early gene promoter and stimulation of transcription from the late gene promoter. We have tested this model by determining directly the occupancy of the T-antigen binding site in the origin of replication of the late transcription complex. Thus, viral transcription complexes were digested with BglI, a restriction enzyme that cuts in the viral replication origin. The enzyme cleaved 78(+/- 12)% of the late transcription complexes. Control experiments demonstrated that cleavage is blocked when T-antigen is bound to the origin site, that exogenously added T-antigen can bind to the site in the transcription complex, and that T-antigen is not released during isolation of the complex. These results indicate that most of the late transcription complexes do not have T-antigen bound to the origin site, and are therefore inconsistent with models that require this site to be occupied by T-antigen to maintain proper regulation of gene transcription late in infection.

Locations of nucleosomes on the regulatory region of simian virus 40 chromatin

We have asked where the nucleosomes are located with respect to the replication origin and regulatory region of simian virus 40 DNA, what would be the possible functional consequences of the identified locations, and to what extent these locations correlate with the current views on mechanisms involved in establishing nucleosome-free regions in chromatin. To identify the precise location of nucleosomes, we have shot-gun cloned and sequenced nucleosomal DNA obtained from micrococcal nuclease digestion of wt776 chromatin prepared late in infection. Our results indicate that nucleosomes do not occupy unique positions over the replication origin or the elements involved in transcriptional control. However, it appears that the nucleosome distribution is not random, since several nucleosomes are represented by two or more independently generated clones. Two nearly identical cloned fragments map over the replication origin; five include 1.5 copies of the 72 base-pair enhancer sequences; and eight map to a region that spans a DNA bending locus and the major transcription initiation site of the late genes. The complex nucleosome distribution pattern observed in our direct analysis suggests that disparate nucleosome-free regions may be involved in controlling replication, and selective expression of the viral early or late genes.

In vivo assessment of the Z-DNA-forming potential of d(CA.GT)n and d(CG.GC)n sequences cloned into SV40 minichromosomes

Alternating repeated d(CA.GT)n and d(CG.GC)n sequences constitute a significant proportion of the simple repeating elements found in eukaryotic genomic DNA. These sequences are known to form left-handed Z-DNA in vitro. In this paper, we have addressed the question of the in vivo determination of the Z-DNA-forming potential of such sequences in eukaryotic chromatin. For this purpose, we have investigated the ability of a d(CA.GT)30 sequence and a d(CG.GC)5 sequence to form left-handed Z-DNA when cloned into simian virus 40 (SV40) minichromosomes at two different positions: the TaqI site, which occurs in the intron of the T-antigen gene, and the HpaII site, which is located in the late promoter region within the SV40 control region. Formation of Z-DNA at the inserted repeated sequences was analyzed through the change in DNA linkage associated with the B to Z transition. Our results indicate that regardless of: (1) the site of insertion (either TaqI or HpaII), (2) the precise moment of the viral lytic cycle (from 12 h to 48 h postinfection) and (3) the condition of incorporation of the SV40 recombinants to the host cells (either as minichromosomes or as naked DNA, relaxed or negatively supercoiled), neither the d(CA.GT)30 nor the d(CG.GC)5 sequence are stable in the left-handed Z-DNA conformation in the SV40 minichromosome. The biological relevance of these results is discussed.

The ultrastructure of upstream and downstream regions of an active Balbiani ring gene

When active, the 37 kb Balbiani ring genes are known to form transcription loops with an almost fully extended chromatin axis. Here we examine the upstream and downstream regions of such transcription loops by electron microscopy. We demonstrate that a loop starts and ends in tightly packed chromatin; the two anchoring sites are clearly separated from each other in space. The upstream, nontranscribed region consists of a thin, extended, apparently flexible and nucleosome-free fiber corresponding to about 0.5 kb DNA. The downstream, nontranscribed region appears as a 200 nm long nucleofilament loosely coiled into a short, thick chromatin fiber and estimated to contain about 3 kb DNA.

A nuclease-hypersensitive region forms de novo after chromosome replication

Regular nucleosome arrays in eucaryotic chromosomes are punctuated at specific locations, such as active promoters and replication origins, by apparently nucleosome-free sites, also called nuclease-hypersensitive, or exposed, regions. The -400-base pair-exposed region within simian virus 40 (SV40) chromosomes is present in approximately 20% of the chromosomes in lytically infected cells and encompasses the replication origin, transcriptional enhancer, and both late and early SV40 promoters. We report that nearly all SV40 chromosomes lacked the exposed region during replication and that newly formed chromosomes acquired the exposed region of the same degree as did bulk SV40 chromosomes within 1 h after replication. Furthermore, a much lower but significant level of exposure was detectable in late SV40 replication intermediates, indicating that formation of the exposed region could start within minutes after passage of the replication fork.

Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes

The promoter for eukaryotic genes transcribed by RNA polymerase B can be divided into the TATA box (located at -30) and startsite (+1), the upstream element (situated between -40 and about -110), and the enhancer (no fixed position relative to the startsite). Trans-acting factors, which bind to these elements, have been identified and at least partially purified. The role of the TATA box is to bind factors which focus the transcription machinery to initiate at the startsite. The upstream element and the enhancer somehow modulate this interaction, possibly through direct protein-protein interactions. Another class of transcription factors, typified by viral proteins such as the adenovirus EIA products, do not appear to require binding to a particular DNA sequence to regulate transcription. The latest findings in these various subjects are discussed.

A nuclease-hypersensitive region forms de novo after chromosome replication

Regular nucleosome arrays in eucaryotic chromosomes are punctuated at specific locations, such as active promoters and replication origins, by apparently nucleosome-free sites, also called nuclease-hypersensitive, or exposed, regions. The -400-base pair-exposed region within simian virus 40 (SV40) chromosomes is present in approximately 20% of the chromosomes in lytically infected cells and encompasses the replication origin, transcriptional enhancer, and both late and early SV40 promoters. We report that nearly all SV40 chromosomes lacked the exposed region during replication and that newly formed chromosomes acquired the exposed region of the same degree as did bulk SV40 chromosomes within 1 h after replication. Furthermore, a much lower but significant level of exposure was detectable in late SV40 replication intermediates, indicating that formation of the exposed region could start within minutes after passage of the replication fork.

The obtention of simian virus 40 recombinants carrying d(CG.GC)n, d(CA.GT)n and d(CT.GA)n sequences. Stability of the inserted simple repeating sequences

A general strategy for the introduction of simple repeating DNA sequences into the simian virus 40 (SV40) has been developed. SV40 recombinants carrying d(CG.GC)5, d(CA.GT)30 or d(CT.GA)22 insertions at either the TaqI site (position 4739) or the HpaII site (position 346) were obtained and the stability of the inserted DNA sequences studied. The palindromic potentially Z-DNA-forming d(CG.GC)n sequence was found to be highly unstable when compared to either d(CA.GT)n or d(CT.GA)n.

Restriction enzyme accessibility and RNA polymerase localization on transcriptionally active SV40 minichromosomes isolated late in infection

The transcriptionally active SV40 minichromosomes isolated late in infection contain a nucleosome-free ORI region or gap. To analyze the chromatin structure of this subpopulation of minichromosomes extracted at different ionic strengths in the early and late coding regions, minichromosomes were isolated in the presence of a 5, 50, or 130 mM concentration of monovalent cations and subjected to in vitro RNA elongation in either the presence or the absence of high salt and anionic detergent. The minichromosomes isolated at low ionic strength were transcriptionally more active than those isolated at physiological ionic strength. Nevertheless, in each case, the in vitro elongation complexes were present essentially on the late strand of the SV40 genome and localized preferentially in the late and 3' early coding regions. These regions were transcribed similarly in either the presence or the absence of chromatin denaturing agents. In contrast, the in vitro elongation activity of the RNA polymerase molecules present on the late strand in the middle and 5' end of the early coding region was inhibited in the absence of treatments to disrupt chromatin structure. In addition, as probed by restriction enzyme digestion, the ORI and late coding regions of the transcriptionally active minichromosomes were found to be more sensitive than the 5' region of the early genes. Taken together, these results suggest that the 5' and middle regions of the early genes of the SV40 transcriptional complexes isolated late in infection at low or physiological ionic strength are packaged in a more compact conformation than the rest of the genome.

Characterization of SV40 chromatin by mass determination on STEM

Direct mass determination of purified SV40 minichromosomes was obtained by scanning transmission electron microscopy. Twenty to thirty percent of the minichromosomes were found with an Mr of 6.9 +/- 0.4 X 10(6). The rest of the molecules formed a spread Mr distribution ranging from 7.3 X 10(6) to 9.5 X 10(6) due possibly to different contents of the virus-coded proteins, mainly VP1. The apparent mass histogram of individual SV40 nucleosomes presents three maxima at Mr 2.1 X 10(5), 2.6 X 10(5) and 3.1 X 10(5) that could correspond to partially unravelled nucleosomes, complete nucleosomes and complete nucleosomes with the addition of VP1. Beaded structures with a higher mass were also measured; some were found at either side of the open nucleosome-free region.

Transcriptionally active SV40 minichromosomes are restriction enzyme sensitive and contain a nucleosome-free origin region

A nucleosome-free region or gap containing the origin of replication and the transcriptional promoter elements is observed on 20 to 25% of the SV40 minichromosomes isolated at physiological ionic strength late in infection. We used the preferential sensitivity of the gapped minichromosomes to restriction enzymes to obtain sucrose gradient fractions containing 50 to 80% of gapped molecules. The same fractions are also enriched in RNA polymerase B (II) molecules engaged in transcription. Using electron microscopy, we demonstrate here that the transcriptional complexes are preferentially sensitive to restriction enzyme digestion, which indicate that they represent a subpopulation of the gapped minichromosomes.