Characterization of the repressed 5S DNA minichromosomes assembled in vitro with a high-speed supernatant of Xenopus laevis oocytes

Interplay between Alba and Cren7 Regulates Chromatin Compaction in Sulfolobus solfataricus

Chromatin compaction and regulation are essential processes for the normal function of all organisms, yet knowledge on how archaeal chromosomes are packed into higher-order structures inside the cell remains elusive. In this study, we investigated the role of archaeal architectural proteins Alba and Cren7 in chromatin folding and dynamics. Atomic force microscopy revealed that Sulfolobus solfataricus chromatin is composed of 28 nm fibers and 60 nm globular structures. In vitro reconstitution showed that Alba can mediate the formation of folded DNA structures in a concentration-dependent manner. Notably, it was demonstrated that Alba on its own can form higher-order structures with DNA. Meanwhile, Cren7 was observed to affect the formation of Alba-mediated higher-order chromatin structures. Overall, the results suggest an interplay between Alba and Cren7 in regulating chromatin compaction in archaea.

Beads on a string-nucleosome array arrangements and folding of the chromatin fiber

Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes.

Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions

Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA-protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA-protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.

Biochemical analyses of nuclear receptor-dependent transcription with chromatin templates

Chromatin, the physiological template for transcription, plays important roles in gene regulation by nuclear receptors (NRs). It can (1) restrict the binding of NRs or the transcriptional machinery to their genomic targets, (2) serve as a target of regulatory posttranslational modifications by NR coregulator proteins with histone-directed enzymatic activities, and (3) function as a binding scaffold for a variety of transcription-related proteins. The advent of in vitro or "cell-free" systems that accurately recapitulate ligand-dependent transcription by NRs with chromatin templates has allowed detailed analyses of these processes. Biochemical studies have advanced our understanding of the mechanisms of gene regulation, including the role of ligands, coregulators, and nucleosome remodeling. In addition, they have provided new insights about the dynamics of NR-mediated transcription. This chapter reviews the current methodologies for assembling, transcribing, and analyzing chromatin in vitro, as well as the new information that has been gained from these studies.

Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics

We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening-closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy difference between core histone octamers on and off DNA. Addition of ATP led to highly dynamic behavior with time courses exhibiting processive runs of assembly and disassembly not observed in the ATP-depleted case. With ATP present, application of forces of 2 pN led to nearly complete fiber disassembly. Our study suggests that ATP hydrolysis plays a major role in nucleosome rearrangement and removal and that chromatin in vivo may be subject to highly dynamic assembly and disassembly processes that are modulated by DNA tension.

In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system

An extensive set of analyses of the yeast PHO5 gene, mostly performed in vivo, has made this gene a model for the role of chromatin structure in gene regulation. In the repressed state, the PHO5 promoter shows a characteristic chromatin organization with four positioned nucleosomes and a short hypersensitive site. So far the basis for this nucleosome positioning has remained unresolved. We have therefore decided to complement the in vivo studies by an in vitro approach. As a first step, we have asked whether the characteristic PHO5 promoter chromatin structure depends on the cellular context including replication or higher order nuclear chromatin organization or whether it can be reconstituted in vitro in a cell-free system. To this end we have established an in vitro chromatin assembly system based on yeast extracts. It is capable of generating extensive regular nucleosomal arrays with physiological spacing. Assembly requires supplementation with exogenous histones and is dependent on energy leading to chromatin with dynamic properties due to ATP-dependent activities of the extract. Using the PHO5 promoter sequence as template in this replication independent system, we obtain a nucleosomal pattern over the PHO5 promoter region that is very similar to the in vivo pattern of the repressed state. This shows that the chromatin structure at the PHO5 promoter represents a self-organizing system in cell-free yeast extracts and provides a promising substrate for in vitro studies with a direct in vivo correlate.

Xenopus transcription factor IIIA and the 5S nucleosome: development of a useful in vitro system

5S RNA genes in Xenopus are regulated during development via a complex interplay between assembly of repressive chromatin structures and productive transcription complexes. Interestingly, 5S genes have been found to harbor powerful nucleosome positioning elements and therefore have become an important model system for reconstitution of eukaryotic genes into nucleosomes in vitro. Moreover, the structure of the primary factor initiating transcription of 5S DNA, transcription factor IIIA, has been extensively characterized. This has allowed for numerous studies of the effect of nucleosome assembly and histone modifications on the DNA binding activity of a transcription factor in vitro. For example, linker histones bind 5S nucleosomes and repress TFIIIA binding in vitro in a similar manner to that observed in vivo. In addition, TFIIIA binding to nucleosomes assembled with 5S DNA is stimulated by acetylation or removal of the core histone tail domains. Here we review the development of the Xenopus 5S in vitro system and discuss recent results highlighting new aspects of transcription factor - nucleosome interactions,

Multiple ISWI ATPase complexes from xenopus laevis. Functional conservation of an ACF/CHRAC homolog

The nucleosomal ATPase ISWI is the catalytic subunit of several protein complexes that either organize or perturb chromatin structure in vitro. This work reports the cloning and biochemical characterization of a Xenopus ISWI homolog. Surprisingly, whereas we find four complex forms of ISWI in egg extracts, we find no functional homolog of NURF. One of these complexes, xACF, consists of ISWI, Acf1, and a previously uncharacterized protein of 175 kDa. Like both ACF and CHRAC, this complex organizes randomly deposited histones into a regularly spaced array. The remaining three forms include two novel ISWI complexes distinct from known ISWI complexes plus a histone-dependent ATPase complex. This comprehensive biochemical characterization of ISWI underscores the evolutionary conservation of the ACF/CHRAC family.

Histone octamer dissociation is not required for in vitro replication of simian virus 40 minichromosomes

Replication of chromosomal templates requires the passage of the replication machinery through nucleosomally organized DNA. To gain further insights into these processes we have used chromatin that was reconstituted with dimethyl suberimidate-cross-linked histone octamers as template in the SV40 in vitro replication system. By supercoiling analysis we found that cross-linked histone octamers were reconstituted with the same kinetic and efficiency as control octamers. Minichromosomes with cross-linked nucleosomes were completely replicated, although the efficiency of replication was lower compared with control chromatin. Analysis of the chromatin structure of the replicated DNA revealed that the cross-linked octamer is transferred to the daughter strands. Thus, our data imply that histone octamer dissociation is not a prerequisite for the passage of the replication machinery and the transfer of the parental nucleosomes.

A method for efficient extraction of bovine papilloma virus-based minichromosomes that preserves native chromatin structure

Aiming to create an adequate model for investigation of the molecular mechanisms involved in transcriptional regulation by steroid hormones, a number of cell lines carrying bovine papilloma virus (BPV) based constructs containing the mouse mammary tumor virus long terminal repeat (LTR) were established (Ostrowski et al., Mol. Cell. Biol. 3, 2945-2957, 1983). However, all our attempts to extract from the cells such minichromosomes as nucleoprotein complexes using a method previously described (Ostrowski, Nucleic Acids Res. 15, 6957-6971, 1987) failed. Here, we show that this failure was attributable to DNA rearrangements in most of the cell lines, resulting in the integration of the BPV-based constructs into the host cell genome. We have identified two cell lines where the constructs are episomal. Micrococcal nuclease digestion of the nuclei demonstrated the presence of nucleosomes positioned over the episomal MMTV LTR. We managed to optimize conditions for preparation of nuclei and minichromosomes, which allowed extraction of approximately 40% of the minichromosomes, most of them being in circular superhelical form. Our data show clearly that the main factor preventing the release of minichromosomes from the nuclei is the presence of polyamines in the cell lysis buffer. The organization of MMTV promoter chromatin was unaffected by the extraction procedure, suggesting that these minichromosomes could be valuable templates for in vitro transcription studies and to identify proteins involved in chromatin remodeling during transcription.

The yeast RAD7 and RAD16 genes are required for postincision events during nucleotide excision repair. In vitro and in vivo studies with rad7 and rad16 mutants and purification of a Rad7/Rad16-containing protein complex

In eukaryotes, nucleotide excision repair (NER) is a complex reaction requiring multiple proteins. In the yeast Saccharomyces cerevisiae, two of these proteins, Rad7 and Rad16, are specifically involved in the removal of lesions from transcriptionally silent regions of the genome in vivo. Extracts prepared from rad7 or rad16 mutant cells are deficient, but not totally defective, in both oligonucleotide excision and repair synthesis of damaged plasmid DNA. We show that these extracts are, however, fully proficient in the incision step of the NER reaction in vitro. Furthermore, using a cdc9 mutant to trap incision intermediates, we demonstrate that rad7 and rad16 mutants are proficient in NER-dependent DNA incision in vivo. A purified protein complex containing both Rad7 and Rad16 proteins complements the oligonucleotide excision and repair synthesis defects in rad7 and rad16 mutant extracts. We conclude that the products of the RAD7 and RAD16 genes are involved in a postincision event(s) during NER in yeast.

The nucleosome: a powerful regulator of transcription

Nucleosomes provide the architectural framework for transcription. Histones, DNA elements, and transcription factors are organized into precise regulatory complexes. Positioned nucleosomes can facilitate or impede the transcription process. These structures are dynamic, reflecting the capacity of chromatin to adopt different functional states. Histones are mobile with respect to DNA sequence. Individual histone domains are targeted for posttranslational modifications. Histone acetylation promotes transcription factor access to nucleosomal DNA and relieves inhibitory effects on transcriptional initiation and elongation. The nucleosomal infrastructure emerges as powerful contributor to the regulation of gene activity.

Nucleosome assembly activity and intracellular localization of human CAF-1 changes during the cell division cycle

We characterized changes of nucleosome assembly activity, intracellular localization, and reversible phosphorylation of the human chromatin assembly factor CAF-1 during the somatic cell division cycle. HeLa cells were synchronized in the G1, S, G2, and M phases of the cell cycle. All three subunits of human CAF-1 (p150, p60, and p48) are present during the entire cell cycle. In interphase, p150 and p60 are bound to the nucleus, but they predominantly dissociate from chromatin during mitosis. During S phase, p150 and p60 are concentrated at sites of intranuclear DNA replication. Only a fraction of total p48 is associated with p150 and p60, and the majority is present in other high molecular weight complexes. The other nucleosome assembly protein, NAP-1, is predominantly cytosolic throughout the cell cycle. Human CAF-1 efficiently mediates nucleosome assembly during complementary DNA strand synthesis in G1, S, and G2 phase cytosolic extracts. Active CAF-1 can be isolated as a 6.5 S complex from G1, S, and G2 phase nuclei. In contrast, CAF-1 isolated from mitotic cytosol does not support nucleosome assembly during DNA synthesis. In mitosis, the p60 subunit of inactive CAF-1 is hyperphosphorylated, whereas active CAF-1 in interphase contains hypophosphorylated and/or phosphorylated forms of p60.

In vitro chromatin assembly of the HIV-1 promoter. ATP-dependent polar repositioning of nucleosomes by Sp1 and NFkappaB

Nuclease hypersensitive sites exist in vivo in the chromatin of the integrated human immunodeficiency virus (HIV)-1 proviral genome, in the 5'-long terminal repeat (LTR) within the promoter/enhancer region near Sp1 and NFkappaB binding sites. Previous studies from the Kadonaga and Jones laboratories have shown that Sp1 and NFkappaB can establish hypersensitive sites in a truncated form of this LTR when added before in vitro chromatin assembly with Drosophila extracts, thus facilitating subsequent transcriptional activation of a linked reporter gene upon the association of additional factors (Pazin, M. J., Sheridan, P. L., Cannon, K., Cao, Z., Keck, J. G., Kadanaga, J. T., and Jones, K. A. (1996) Genes & Dev. 10, 37-49). Here we assess the role of a full-length LTR and 1 kilobase pair of downstream flanking HIV sequences in chromatin remodeling when these transcription factors are added after chromatin assembly. Using Xenopus laevis oocyte extracts to assemble chromatin in vitro, we have confirmed that Sp1 and NFkappaB can indeed induce sites hypersensitive to DNase I, micrococcal nuclease, or restriction enzymes on either side of factor binding sites in chromatin but not naked DNA. We extend these earlier studies by demonstrating that the process is ATP-dependent when the factors are added after chromatin assembly and that histone H1, AP1, TBP, or Tat had no effect on hypersensitive site formation. Furthermore, we have found that nucleosomes upstream of NFkappaB sites are rotationally positioned prior to factor binding and that their translational frame is registered after binding NFkappaB. On the other hand, binding of Sp1 positions adjacent downstream nucleosome(s). We term this polar repositioning because each factor aligns nucleosomes only on one side of its binding sites. Mutational analysis and oligonucleotide competition each demonstrated that this remodeling required Sp1 and NFkappaB binding sites.

Yeast chromatin reconstitution system using purified yeast core histones and yeast nucleosome assembly protein-1

Transcription regulation in the cell occurs in the context of chromatin. It follows that a thorough investigation of the mechanism of transcription regulation must take into account the role of chromatin structure. Through classical and molecular genetic experiments in yeast, great strides have been made in understanding the role of chromatin in eukaryotic gene regulation. To achieve a more detailed understanding of the biochemical mechanism of transcription regulation, a yeast chromatin reconstitution system is needed. This need drove us to develop a yeast core histone purification procedure for the reconstitution of these histones into chromatin templates using components wholly derived from yeast. We have purified native yeast core histones in milligram quantities and we have shown these histones to be competent for reconstitution of chromatin templates using yeast nucleosome assembly protein-1. This accomplishment sets the stage for studies using the full power of yeast as an experimental organism to investigate the role of chromatin in transcription regulation.

Dissociation of protamine-DNA complexes by Xenopus nucleoplasmin and minichromosome assembly in vitro

Nucleoplasmin, an acidic thermostable protein abundant in the nucleus of Xenopus laevis oocytes, has been found to dissociate complexes of pUC19 DNA and protein phi 1, an intermediate protamine present in ripe sperm from the mollusc Mytilus edulis. Cruder preparations of nucleoplasmin, such as the amphibian oocyte S150 extract and its thermostable fraction, also dissociate the heterologous DNA-phi 1 complexes and, in addition, promote the assembly of plasmid DNA into a minichromosome displaying regular nucleosomal periodicity, as revealed by micrococcal nuclease digestion. In contrast, purified nucleoplasmin complemented with rat hepatocyte core histone octamers in the presence of DNA topoisomerase I, although capable of inducing nucleoprotein formation onto the complexed DNA, fails to position nucleosomes at the native spacings seen in chromatin in vivo. These data favour the existence of a general mechanism to bring about, in a concerted manner, removal of sperm-specific nuclear proteins and reconstitution of somatic chromatin following fertilization.

DNA knotting abolishes in vitro chromatin assembly

Topological knots can be formed in vitro by incubating covalently closed double stranded DNA and purified topoisomerase II from the yeast Saccharomyces cerevisiae in an ATP-dependent reaction. Knotting production requires a starting enzyme/DNA mass ratio of 1. Analysis of knotted DNA was carried out by using both one- and two-dimensional agarose gel electrophoresis. The knots generated are efficiently untied, and give relaxed DNA rings, by catalytic amounts of topoisomerase II, but not by topoisomerase I. Time course analysis shows the knotting formation over relaxed and supercoiled DNA. When supercoiled DNA was used as a susbtrate, knots appear immediately whereas no transient relaxed rings were observed. The cell-free extract from Xenopus oocytes S-150 cannot assemble nucleosomes on knotted DNA templates as revealed by topological and micrococcal nuclease analysis. Nevertheless, the presence of knotted DNA templates does not inhibit the assembly over the relaxed plasmid. Finally, a pretreatment of knotted DNA with trace amounts of topoisomerase II before the addition of the S-150 yields a canonical minichromosome assembled in vitro. Taking into account these results, I suggest a mechanism of chromatin assembly regulation directed by topoisomerase II.

High mobility group protein 14 and 17 can prevent the close packing of nucleosomes by increasing the strength of protein contacts in the linker DNA

High mobility group (HMG) proteins 14 and 17 are abundant chromatin-associated proteins found in all higher eukaryotic nuclei. This observation demonstrates that HMGs 14 and 17 must have an important and universal function with regard to the structure and function of chromatin. What this function is, including how they interact with a nucleosomal array in vivo, is not known. Recently, we have demonstrated that HMGs 14 and 17 can organize nucleosomes into a regular array and increase the repeat length from 145 to about 160-165 base pairs in vitro. In addition, they can increase the apparent repeat length of chromatin deficient in histones H2A/H2B from 125 to approximately 145 base pairs. Importantly, this template was transcriptionally active. In this study, we report five new observations that begin to address the mechanism by which HMGs 14 and 17 space nucleosomal particles. First, we demonstrate that both human placenta HMG 14 and HMG 17 can space nucleosomes to produce a chromatin template with a repeat length around 160 base pairs. This result further highlights the similarity between these proteins in terms of protein structure and perhaps function. Second, we show that digestion of HMG containing chromatin with micrococcal nuclease produces DNA fragments that were approximately 10 and 20 base pairs longer than nucleosome core-particle DNA. This suggests that HMG 14 or HMG 17 can protect, directly or indirectly, at least an additional 10 base pairs of linker DNA from micrococcal digestion. However, this HMG-containing particle does not produce a strong kinetic block, and further digestion results in the eventual accumulation of DNA fragments 145 base pairs in length. Third, by comparing the full-length protein with different domains, we demonstrate that the acidic carboxyl-terminal domain is absolutely required for nucleosome spacing, neither the nucleosome binding domain of HMG 14 or HMG 17 nor the amino-terminal domain plus the nucleosome binding domain of HMG 14 could space nucleosomes. Fourth, we demonstrate that extensive micrococcal nuclease digestion of chromatin deficient in histones H2A/H2B led to the accumulation of DNA fragments about 110 base pairs in length, which is presumably the length of DNA associated with a nucleosomal particle deficient in one H2A/H2B dimer. Incorporation of either HMG 14 or HMG 17 into this chromatin results in the disappearance of this band and increase in the accumulation of fragments around 140-150 base pairs in length. Finally, in contrast to spacing of complete nucleosomes, we find that the nucleosome binding domain of HMG 17 (but not the nucleosome binding of HMG 14) is the only domain required for spacing of H2A/H2B-deficient chromatin.

Binding of histone H1 to DNA is indifferent to methylation at CpG sequences

The possibility that histone H1 binds preferentially to DNA containing 5-methylcytosine in the dinucleotide CpG is appealing, as it could help to explain the repressive effects of methylation on gene activity. In this study, the affinity of purified H1 for methylated and non-methylated DNA sequences has been tested using both naked DNA and chromatin. Based on a variety of assays (bandshifts, filter-binding assays, Southwestern blots, and nuclease sensitivity assays), we conclude that H1 has no significant preference for binding to naked methylated DNA. Similarly, H1 showed the same affinities for methylated and non-methylated DNA when assembled into chromatin in a Xenopus oocyte extract. Thus potential cooperative interaction of H1 with polynucleosomal complexes is not enhanced by the presence of DNA methylation.

The interaction of transcription factors with nucleosomal DNA

Nucleosome positioning is proposed to have an essential role in facilitating the regulated transcription of eukaryotic genes. Some transcription factors can bind to DNA when it is appropriately wrapped around the histone core, others cannot bind due to the severe deformation of DNA structure. The staged assembly of nucleosomes and positioning of histone-DNA contacts away from promoter elements can facilitate the access of transcription factors to DNA. Positioned nucleosomes can also facilitate transcription through providing the appropriate scaffolding to bring regulatory factors bound at dispersed sites into juxtaposition.

Effects of plasmid length and positioned nucleosomes on chromatin assembly in vitro

Histone H5 induces extensive nucleosome alignment in vitro, with a 210 +/- 5 base pair (bp) average unit repeat, on some of the constructs derived from plasmid pBR327. Plasmid pBR327 itself aligns nucleosomes poorly, even though it possesses a chromatin organizing region which nucleates the alignment reaction [Jeong et al. (1991) J. Mol. Biol. 222, 1131-1147]. Examination of various regions of pBR327 chromatin by Southern hybridization revealed no substantial regional differences, suggesting an essentially all-or-none alignment mechanism. Twenty-four pBR327 deletion constructs, with the chromatin organizing region intact, were analyzed for nucleosome alignment in vitro, in addition to the six previously described. Although nucleosome alignment on plasmids of size greater than 5 kb was not affected by small length changes, circular plasmids with total lengths between 2400 and 3600 bp generally permitted alignment only when their lengths were close to integer multiples of 210 +/- 3 bp. The measured repeat lengths for the large plasmids and the smaller ones that aligned nucleosomes were all 210 bp, within experimental precision. The failure of two approximately 3.2-kb plasmids to align nucleosomes, even though their lengths were close to 15 x 210 bp, could be attributed to the effects of four strongly positioned nucleosomes that form on pBR327 sequences. Evidence is provided that nucleosome arrays can be quasicrystalline and are capable of transmitting information over a distance of more than 2 kb.

Kinetic control of 5 S RNA gene transcription

We have determined that the differential transcription of somatic and oocyte-type 5 S RNA genes in a Xenopus laevis oocyte extract is a consequence of vastly different rates of stable complex assembly. Somatic-type 5 S RNA genes sequester a limiting transcription factor much more rapidly than oocyte-type 5 S RNA genes. Once formed, however, transcription complexes on both types of genes are stable, and are transcribed at nearly equivalent rates. The relative rates of stable transcription complex assembly are strongly dependent on the concentration of Mg2+. Kinetic differences in transcription complex assembly provides a key distinguishing feature between these two genes which may be used in the selective repression of oocyte-type 5 S RNA genes during the early development of Xenopus, and may also be utilized in other systems of regulated gene expression.

Influence of chromatin folding on transcription initiation and elongation by RNA polymerase III

Nucleosomes were assembled onto either closed circular plasmids containing a single Xenopus 5S RNA gene or a linear tandemly repeated array of Lytechinus 5S RNA genes. Both chromatin templates were found to vary in their extent of compaction, depending upon the type and concentration of cation in solution. Compaction of these chromatin templates led to a significant inhibition of both transcription initiation and elongation by RNA polymerase III. Thus, the transcriptional repression observed after incorporation of genes into chromatin depends not only on occlusion of the promoter elements through direct contact with histones but also on compaction of nucleosomal arrays which occurs under the conditions of the transcription reactions.

Renaturation of DNA catalysed by yeast DNA repair and recombination protein RAD10

The RAD10 gene of Saccharomyces cerevisiae is required for the incision step of excision repair of ultraviolet-damaged DNA, and it functions in mitotic recombination. RAD10 has homology to the human excision repair gene ERCC-1. Here we describe the purification of the protein encoded by RAD10 and show that it is a DNA-binding protein with a strong preference for single-stranded DNA. We also show that RAD10 promotes the renaturation of complementary DNA strands.

Chromatin replication

Just as the faithful replication of DNA is an essential process for the cell, chromatin structures of active and inactive genes have to be copied accurately. Under certain circumstances, however, the activity pattern has to be changed in specific ways. Although analysis of specific aspects of these complex processes, by means of model systems, has led to their further elucidation, the mechanisms of chromatin replication in vivo are still controversial and far from being understood completely. Progress has been achieved in understanding: 1. The initiation of chromatin replication, indicating that a nucleosome-free origin is necessary for the initiation of replication; 2. The segregation of the parental nucleosomes, where convincing data support the model of random distribution of the parental nucleosomes to the daughter strands; and 3. The assembly of histones on the newly synthesized strands, where growing evidence is emerging for a two-step mechanism of nucleosome assembly, starting with the deposition of H3/H4 tetramers onto the DNA, followed by H2A/H2B dimers.

Chromatin assembly on plasmid DNA in vitro. Apparent spreading of nucleosome alignment from one region of pBR327 by histone H5

We have found that histone H5 (or H1) induces physiological nucleosome spacings and extensive ordering on some plasmid constructions, but not on others, in a fully defined in vitro system. Plasmid pBR327 containing DNA insertions with lengths close to 300 base-pairs permitted histone H5 to induce a remarkable degree of nucleosome alignment. Seventeen multiples of a unit 210(+/- 4) base-pair repeat, covering the entire plasmid, were detected. Plasmid pBR327, not containing a DNA insert, permitted continuous alignment of only a few nucleosomes. These observations suggest that a necessary requirement in this system for histone H5 (or H1)-induced nucleosome alignment on small (less than 4 kb; 1 kb = 10(3) bases or base-pairs) circular plasmids may be that the total DNA length must be close to an integer multiple of the nucleosome repeat length generated, a type of boundary effect. Consistent with this hypothesis, five deletion constructs of pBR327 (not containing inserts), that spanned 64% of the plasmid, and possessed DNA lengths close to integer multiples of 210 base-pairs, permitted nucleosome alignment by histone H5. We have also found that plasmid length adjustment is not a sufficient condition for nucleosome alignment. For example, plasmids pBR322 and pUC18 did not permit nucleosome alignment when adjusted to near-integer multiples of 210 base-pairs. Also, for pBR327 that contained a length-adjusted deletion in one particular region, appreciable nucleosome alignment no longer occurred. These data suggest that a contiguous approximately 800 base-pair region of pBR327, interrupted in pBR322 and not present in pUC18, can nucleate histone H5-induced nucleosome alignment, which can then spread to adjacent chromatin. Supporting this idea, a positioned five-nucleosome array appears to originate in the required region. Additionally, on a larger (6.9 kb) plasmid construction, the "chromatin organizing region" of pBR327 and adjacent DNA on one side of it exhibited preferred H5-induced nucleosome alignment.

Inhibition of 5S RNA transcription in vitro by nucleosome cores with low or high levels of histone acetylation

Nucleosomes exert strong inhibitory effects on gene transcription in vitro and in vivo. Since most DNA is packaged in nucleosomes, there must exist mechanisms to alleviate this inhibition during gene activation. Nucleosomes could be destabilized by histone acetylation which is strongly correlated with gene expression. We have compared the effects of nucleosomes cores with low or high levels of histone acetylation on 5S RNA transcription with Xenopus nuclear extracts in vitro. Little or no difference was observed over a range of 1 to 15 nucleosome cores per plasmid template. This result suggests that nucleosomal DNA is not more accessible to transcription factors and to the transcription machinery in acetylated nucleosomes.

An analysis of transcription factor TFIIIA-mediated DNA supercoiling

We have analyzed transcription factor-mediated DNA supercoiling catalyzed by the Xenopus oocyte extract (S-150). Under conditions that inhibit endogenous supercoiling activity (2 mM EDTA), the 5S RNA specific transcription factor, TFIIIA, promotes a negative change in DNA linking number. The SV40 binding protein, T antigen, appears not to promote DNA supercoiling under these conditions. A nucleosomal ladder can be seen after DNase I digestions only if the DNA template is pre-bound by TFIIIA prior to the addition of the S-150 extract. These studies suggest that TFIIIA may stimulate DNA supercoiling by enhancing the development of protein-DNA interactions via a mechanism that may include nucleosome assembly.

Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes

GAL4 derivatives containing an activation domain alleviated repression of a promoter during nucleosome assembly. A GAL4 derivative lacking an activation domain stably bound the promoter during nucleosome assembly but was not sufficient to preserve promoter function. The activation domain of GAL4 derivatives was essential for preserving promoter function, and thus the transcriptional stimulatory activity attributable to these activation domains increased dramatically during nucleosome assembly. Furthermore, promoter-bound activation domains allowed the formation of preinitiation complexes after nucleosome assembly. Finally, GAL4 derivatives containing activation domains significantly stimulated transcription through bacterially produced yeast TFIID only from nucleosome-assembled templates. These data indicate that acidic activation domains stimulate transcription by enhancing the ability of basal transcription factors to compete with nucleosomes for occupancy of the promoter.

Assembly and properties of chromatin containing histone H1

The Xenopus oocyte supernatant (oocyte S-150) forms chromatin in a reaction that is affected by temperature and by the concentration of ATP and Mg. Under optimal conditions at 27 degrees C, relaxed DNA plasmids are efficiently assembled into supercoiled minichromosomes with the endogenous histones H3, H4, H2A and H2B. This assembly reaction is a gradual process that takes four to six hours for completion. Micrococcal nuclease digestions of the chromatin assembled under these conditions generate an extended series of DNA fragments that are, on average, multiples of 180 base-pairs. We have examined the effect of histone H1 in this system. Exogenous histone H1, when added at a molar ratio of H1 to nucleosome of 1:1 to 5:1, causes an increase in the micrococcal nuclease resistance of the chromatin without causing chromatin aggregation under these experimental conditions. Furthermore, the periodically arranged nucleosomes display longer internucleosome distances, and the average length of the nucleosome repeat is a function of the amount of histone H1 added, when this histone is present at the onset of the assembly process. In contrast, no major change in the length of the nucleosome repeat is observed when histone H1 is added at the end of the chromatin assembly process. Protein analyses of the purified minichromosomes show that histone H1 is incorporated in the chromatin that is assembled in the S-150 supplemented with histone H1. The amount of histone H1 bound to chromatin is a function of the total amount of histone H1 added. We define here the parameters that generate histone H1-containing chromatin with native nucleosome repeats from 160 to 220 base-pairs, and we discuss the implications of these studies.

Phosphorylation of sea urchin histone CS H2A

Phosphorylation of cleavage stage (CS) histones was studied during the first cell cycle in male pronuclei of the sea urchin. Histone CS H2A rapidly incorporated 32PO4 during the replication period, but not before. Peptide mapping and amino acid analysis of radiolabelled CS H2A showed that phosphorylation occurred mainly on serine residues located in the C-terminal region of the molecule. When DNA replication was inhibited with aphidicolin both CS H2A and CS H2B accumulated in male pronuclei at the same rate as in the control culture, whereas accumulation of H3 and H4 histones was reduced. Incorporation of 32PO4 by CS H2A doubled when DNA synthesis was inhibited with aphidicolin. Thus phosphorylation of CS H2A was correlated with transport of CS histones from the egg storage pool to the male pronucleus, but not with chromatin synthesis, indicating that this event precedes nucleosome formation. A role for phosphorylation and dephosphorylation of the CS H2A C-terminal region in modulating transport of stored CS histone dimers and their assembly into nucleosomes is discussed.

Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro

The purification and characterization of a replication-dependent chromatin assembly factor (CAF-I) from the nuclei of human cells is described. CAF-I is a multisubunit protein that, when added to a crude cytosol replication extract, promotes chromatin assembly on replicating SV40 DNA. Chromatin assembly by CAF-I requires and is coupled with DNA replication. The minichromosomes assembled de novo by CAF-I consist of correctly spaced nucleosomes containing the four core histones H2A, H2B, H3, and H4, which are supplied in a soluble form by the cytosol replication extract. Thus, by several criteria, the CAF-I-dependent chromatin assembly reaction described herein reflects the process of chromatin formation during DNA replication in vivo.

Large scale isolation of nuclei from oocytes of Xenopus laevis

We describe an improvement on the procedure of Scalenghe et al. (F. Scalenghe, M. Buscaglia, C. Steinheil, and M. Crippa (1978) Chromosoma 66, 299-308) for the large scale isolation of nuclei from Xenopus laevis oocytes. The nuclear extract obtained was tested for its ability to transcribe a cloned Xenopus 5 S RNA gene and for the presence of nuclear factors interacting with a X. laevis ribosomal protein gene promoter. Efficiency of accurate transcription and of factor binding is comparable with that of an extract prepared from manually isolated nuclei.