The structure of chromatin replicated in vitro

Multistep pathway for replication-dependent nucleosome assembly

We have used cell-free DNA replication to study the relationship between DNA replication and chromatin assembly. As others have reported, we find that DNA replication facilitates nucleosome assembly. We show here that replication-dependent nucleosome assembly occurs in at least two steps. The first step requires replicating DNA; the second step occurs after replication has been completed and is promoted by a nuclear extract. Consistent with this multistep model, we observe that the replicated simian virus 40 minichromosome is organized into a repeating array of DNA-protein particles that are structurally distinct from mature nucleosomes. These particles may be precursors in a pathway of nucleosome assembly since in the second, replication-independent step the nuclear extract converts this nascent chromatin into nucleosomes.

Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures

The structure of replicating simian virus 40 (SV40) minichromosomes was studied by DNA crosslinking with trimethyl-psoralen. The procedure was used both in vitro with extracted SV40 minichromosomes as well as in vivo with SV40-infected cells. Both procedures gave essentially the same results. Mature SV40 minichromosomes are estimated to contain about 27 nucleosomes (error +/- 2), except for those molecules with a nucleosome-free gap, which are interpreted to contain 25 nucleosomes (error +/- 2). In replicative intermediates, nucleosomes are present in the unreplicated parental stem with the replication fork possibly penetrating into the nucleosomal DNA before the histone octamer is removed. Nucleosomes reassociate on the newly replicated DNA branches at distances from the branch point of 225 ( +/- 145) nucleotides on the leading strand and of 285( +/- 120) nucleotides on the lagging strand. In the presence of cycloheximide, daughter duplexes contained unequal numbers of nucleosomes, supporting dispersive and random segregation of parental nucleosomes. These were arranged in clusters with normal nucleosome spacing. We detected a novel type of interlocked dimer comprising two fully replicated molecules connected by a single-stranded DNA bridge. We cannot decide whether these dimers represent hemicatenanes or whether the two circles are joined by a Holliday-type structure. The joining site maps within the replication terminus. We propose that these dimers represent molecules engaged in strand segregation.

Chromatin structure and DNA replication

The structure of (3H) thymidine pulse labeled, replicating chromatin differs from that of non replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. We summarize the structural changes that we observe using replicating chromatin as substrate for micrococcal nuclease. The data suggest a more extended configuration of replicating compared to non replicating chromatin. We use these data to discuss a model of the chromatin structure in the vicinity of replication forks. Finally, we present data to show that the reversion of structural changes in replicative chromatin depends on continued DNA replication.

Chromatin maturation depends on continued DNA-replication

The structure of [3H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [3H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. We conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation.

Organization of the newly replicated chromatin in the vicinity of the replication fork

Ehrlich ascites tumour cells were pulse-labelled with [3H]thymidine for 1 min or were treated with cycloheximide and labelled with [3H]thymidine for 45 min. The kinetics of digestion with micrococcal nuclease of both pulse-labelled and cycloheximide chromatins showed that they exhibited increased susceptibility towards the enzyme. At the same time their release from the nucleus was retarded and this was interpreted to mean that, unlike the bulk of chromatin, they were tightly bound to a fixed nuclear structure. When subjected to an equilibrium metrizamide-triethanolamine density gradient centrifugation both pulse-labelled and cycloheximide chromatins banded at higher density than control chromatin, which was an indication of their higher protein to DNA ratio. After a mild trypsinization, eliminating H1 and the nonhistone proteins, the pulse-labelled chromatin sedimented to the same density as control chromatin, and the cycloheximide chromatin sedimented to a density which was intermediate between those of control chromatin and free DNA. This result showed that the newly replicated chromatin had the same, and the cycloheximide chromatin half the amount of core histones present in control chromatin.

Replicative conformation of parental nucleosomes: salt sensitivity of deoxyribonucleic acid-histone interaction and alteration of histone H1 binding

The transiently altered DNA-histone interaction of parental chromatin during replication was studied by micrococcal nuclease digestion. A large amount of nuclease-resistant pulse-labeled DNA and a small fraction of nonreplicating DNA are released from chromatin fragments by treatment with 0.5 M NaCl and appear as protein-free DNA. As shown by reconstitution experiments, the salt sensitivity of digested nascent chromatin is most probably a consequence of the shorter DNA fragment size (55 +/- 15 base pairs) in these complexes. This new DNA is associated with parental chromatin fragments which are structurally changed in such a way that parts of nucleosomal DNA were more susceptible to nuclease attack. The core histones of these particles are probably not distinct from those of salt-stable nucleosomes. However, histone H1 and probably high-mobility group proteins appear to be more weakly bound during replication as shown by electrophoresis under nondenaturing conditions. The results agree with the assumption that the transient alteration of nucleosomal conformation describes a state in which DNA could be replicated without leaving the associated core histone complexes. A possible attachment of pulse-labeled chromatin with nuclear matrix is discussed.

Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease

Replicating simian virus 40 (SV40) chromosomes were found to be similar to other eukaryotic chromosomes in that the rate and extent of micrococcal nuclease (MNase) digestion were greater with replicating than with nonreplicating mature SV40 chromatin. MNase digestion of replicating SV40 chromosomes, pulse labeled in either intact cells or nuclear extracts, resulted in the rapid release of nascent DNA as essentially bare fragments of duplex DNA (3-7S) that had an average length of 120 base pairs and were degraded during the course of the reaction. In addition, nucleosomal monomers, equivalent in size to those from mature chromosomes, were released. On the other hand, MNase digestion of uniformly labeled mature SV40 chromosomes resulted in the release of only nucleosomal monomers and oligomers. The small nascent DNA fragments released from replicating chromosomes represented prenucleosomal DNA (PN-DNA) from the region of replication forks that encompasses the actual sites of DNA synthesis and includes Okazaki fragments. Predigestion of replicating SV40 chromosomes with both Escherichia coli exonuclease III (3'-5') and bacteriophage T7 gene 6 exonuclease (5'-3') resulted in complete degradation of PN-DNA. This result, together with the observation that isolated PN-DNA annealed equally well to both strands of SV40 restriction fragments, demonstrated that PN-DNA originates from both sides of replication forks. Over 90% of isolated Okazaki fragments annealed only to the retrograde DNA template. The characteristics of isolated PN-DNA were assessed by examining its sensitivity to MNase and single strand specific S1 endonuclease, sedimentation behavior before and after deproteinization, buoyant density in CsCl after formaldehyde treatment, and size on agarose gels. In addition, it was observed that MNase digestion of purified SV40 DNA also resulted in the release of a transient intermediate similar in size to PN-DNA, indicating that a DNA-protein complex is not required to account for the appearance of PN-DNA. These and other data provide a model of replicating chromosomes in which DNA synthesis occurs on a region of replication forks that is free of nucleosomes and is designated as prenucleosomal DNA.

A histone H4-specific methyltransferase. Properties, specificity and effects on nucleosomal histones

A histone H4-specific methyltransferase was purified 80-100-fold from nuclei of calf lymphocytes and from calf thymus. Some biochemical properties of the enzyme are described. The enzyme transfers in vitro methyl groups from S-adenosylmethionine preferentially to the lysine residue 20 of histone H4. This is the major in vivo methylation site of H4. DNA-bound or nucleosomal H4 is not methylated in vitro. We have used methylated and unmodified H4 (in the presence of sufficient quantities of the other core histones) for nucleosome reconstitution in vitro and have not found significant differences in the efficiencies of assembly.

Role of cytosol proteins in DNA chain growth and chromatin replication in Friend erythroleukemia cell nuclei

The influence of cytosol proteins on the replication of DNA and chromatin in isolated nuclei from Friend erythroleukemia cells has been investigated. The overall process has been clearly shown to proceed stepwise. In the absence of cytosol proteins DNA chain growth tends to stop after the addition of approximately 200 nucleotides to the ends of growing chains. In the presence of cytosol proteins these sections grow to approximately 250 nucleotides, and participate in the stepwise extension of the replication process through adjacent nucleosomal sections of the template. Immediately following pulse labeling, the newly replicated DNA resides in a chromatin form which appears to be relatively resistant to digestion by micrococcal nuclease. During a chase interval, the association of the pulse-labeled DNA with nuclear proteins matures to a form which yields lengths of DNA upon digestion with micrococcal nuclease that correspond to mono-, di-, tri- and polynucleosomal units of chromatin. In the absence of cytosol proteins the nuclease resistant state of the labeled DNA tends to predominate and persist. The data support the view that DNA replication in a chromosomal setting proceeds stepwise over successive nucleosomal sections of template made accessible by the interaction of the cytosol proteins at or near the replication fork.

Acetylation of nucleosomal histones in vitro

A new histone-specific acetyltransferase, which is closely associated with nucleosomes prepared from lymphocyte nuclei by treatment with micrococcal nuclease, is described. The acetylating enzyme transfers [3H]acetyl groups from [3H]acetyl-coenzyme A to the endogenous histones H2A, H2B, H3 and H4 in nucleosomes as well as to free histones added to the reaction mixture. Histone H1 is not acetylated by this enzyme. The acetyltransferase was partially purified by DEAE-Sephadex and DNA-cellulose chromatography. The nucleosome-associated enzyme binds to DNA cellulose at low salt concentrations (DNA-binding acetyltransferase), while the previously described histone-specific acetyltransferases have no affinity to DNA under these conditions. This high affinity for DNA may explain the association of DNA-binding acetyltransferase with nucleosomes.

Replicative DNA synthesis and unscheduled DNA synthesis in permeable sarcoma cells studied by nuclease digestion

About 20% of DNA replicated in vitro in permeable mouse ascites sarcoma cells showed higher sensitivity to staphylococcal nuclease than the sensitivity of bulk DNA, and the remaining part showed the same nuclease sensitivity as that of parental chromatin DNA. The sensitivity of DNA replicated in permeable cells was higher than that of DNA newly replicated in vivo in intact cells, and close to that of DNA newly replicated in vivo in the presence of cycloheximide. Bleomycin-induced unscheduled DNA synthesis in permeable cells was highly sensitive to the nuclease. The results suggest that DNA replicated in vitro and parental nuclear protein form immature nucleosomes, probably in the same way as in vivo chromatin replication in the presence of protein synthesis inhibitors. It also appears that bleomycin-induced, unscheduled DNA synthesis occurs largely in the internucleosomal region.