Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA

Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation

Extensive studies of the beta-phaseolin (phas) gene in transgenic tobacco have shown that it is highly active during seed embryogenesis but is completely silent in leaf and other vegetative tissues. In vivo footprinting revealed that the lack of even basal transcriptional activity in vegetative tissues is associated with the presence of a nucleosome that is rotationally positioned with base pair precision over three phased TATA boxes present in the phas promoter. Positioning is sequence-dependent because an identical rotational setting is obtained upon nucleosome reconstitution in vitro. A comparison of DNase I and dimethyl sulfate footprints in vivo and in vitro strongly suggests that this repressive chromatin architecture is remodeled concomitant with gene activation in the developing seed. This leads to the disruption of histone-mediated DNA wrapping and the assembly of the TATA boxes into a transcriptionally competent nucleoprotein complex.

Nucleosome translational position, not histone acetylation, determines TFIIIA binding to nucleosomal Xenopus laevis 5S rRNA genes

We sought to study the binding constraints placed on the nine-zinc-finger protein transcription factor IIIA (TFIIIA) by a histone octamer. To this end, five overlapping fragments of the Xenopus laevis oocyte and somatic 5S rRNA genes were reconstituted into nucleosomes, and it was subsequently shown that nucleosome translational positioning is a major determinant of the binding of TFIIIA to the 5S rRNA genes. Furthermore, it was found that histone acetylation cannot override the TFIIIA binding constraints imposed by unfavorable translational positions.

The histone binding protein nucleoplasmin does not facilitate binding of transcription factor IIIA to nucleosomal Xenopus laevis 5S rRNA genes

In an attempt to understand the mechanism by which transcription factors compete with histone octamers for cognate binding sites in chromatin, the effect of the histone binding protein nucleoplasmin on the binding of TFIIIA to nucleosomal 5S rRNA genes was tested. In this study, it was shown that, despite the previously reported nucleosome remodeling ability of nucleoplasmin, the binding of TFIIIA to nucleosomal DNA cannot be facilitated by this protein. Furthermore, it was demonstrated that nucleoplasmin cannot overcome nucleosome mediated repression of transcription of reconstituted 5S rRNA genes. In contrast to earlier work, this study used a homologous system composed of the 5S rRNA gene, nucleoplasmin, and TFIIIA from Xenopus laevis.

Nucleosome positioning by the winged helix transcription factor HNF3

Nucleosome positioning at genetic regulatory sequences is not well understood. The transcriptional enhancer of the mouse serum albumin gene is active in liver, where regulatory factors occupy their target sites on three nucleosome-like particles designated N1, N2, and N3. The winged helix transcription factor HNF3 binds to two sites near the center of the N1 particle. We created dinucleosome templates using the albumin enhancer sequence and found that site-specific binding of HNF3 protein resulted in nucleosome positioning in vitro similar to that seen in liver nuclei. Thus, binding of a transcription factor can position an underlying nucleosome core.

Uncurved-DNA signals are important for translational positioning of nucleosomes

We describe here a possible mechanism for non-random arrangement of nucleosomes along genomic DNA by short stretches of uncurved DNA. Available biochemical data on nucleosome positioning on different DNA sequences were analyzed. A strong correlation between location of nucleosome borders and location of uncurved sequences along DNA was observed. Tested sequences include satellites, 5S RNA genes and 5' regions of different genes.

Transcription factor access to chromatin

The question of how sequence-specific transcription factors access their cognate sites in nucleosomally organized DNA is discussed on the basis of genomic footprinting data and chromatin reconstitution experiments. A classification of factors into two categories is proposed: (i) initiator factors which are able to bind their target sequences within regular nucleosomes and initiate events leading to chromatin remodelling and transactivation; (ii) effector factors which are unable to bind regular nucleosomes and depend on initiator factors or on a pre-set nucleosomal structure for accessing their target sequences in chromatin. Studies with the MMTV promoter suggest that the extent and number of protein-DNA contacts determine whether a factor belongs to one or the other category. Initiator factors have only a few DNA contacts clustered on one side of the double helix, whereas effector factors have extensive contacts distributed throughout the whole circumference of the DNA helix. Thus, the nature of DNA recognition confers to sequence-specific factors their specific place in the sequential hierarchy of gene regulatory events.

In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins

Increasingly, biochemical analyses of processes that occur within eukaryotic nuclei such as transcription and replication require the construction of specific chromatin substrates. Nucleosome complexes reconstituted in vitro have been key elements in a variety of recent studies of polymerase progression and trans-acting factor binding activities. Reconstituted complexes can be easily constructed from purified components in quantities suitable for biochemical and biophysical studies. In addition, reconstituted mononucleosome complexes exhibit native biochemical and biophysical properties but necessarily contain much less heterogeneity with regard to both protein and DNA components than bulk complexes isolated from natural sources. This review details the protocols for reconstitution of model mononucleosome complexes that contain unique DNA sequences and specifically tailored core histone proteins and describes common pitfalls associated with these procedures.

The role of chromatin in transcriptional regulation

Transcriptional activation is mediated by the facilitated binding of the basal transcription complex to the transcription start site of a promoter. The activation procedure involves protein-protein interactions between specific transcription factors and members of the basal transcription complex. However, since eukaryotic DNA is packaged with histones into nucleosomes the accessibility of the transcription factors is limited. In order to activate transcription, some of the specific transcription factors must have the capacity to bind to their binding sites when organized into nucleosomes. As a next step, the chromatin structure of the promoter needs to be decondensed in order to facilitate the binding of the basal transcription machinery. Recent data have addressed these issues and both binding of transcription factors to their chromatin binding site as well as transcription factor-induced chromatin remodelling have been demonstrated. In addition, factors that are candidates to mediate the chromatin remodelling have recently been identified and characterized. The ability of a transcription factor to recognize its cognate element in a nucleosome is an inheret property that differs among different transcription factors. The implications of the rotational and translational positioning of the DNA within a nucleosome on the accessibility of a transcription factor is described in this review. In addition, nucleosome rearrangement and juxtaposing in the context of transcriptional activation is also discussed.

Identification and characterization of genomic nucleosome-positioning sequences

Positioned nucleosomes are believed to play important roles in transcriptional regulation and for the organization of chromatin in cell nuclei. Here, we have isolated the DNA segments in the mouse genome that form the most stable nucleosomes yet characterized. In separate molecules we find phased runs of three to four adenine nucleotides, extensive CA repeats, and in a few cases phased TATA tetranucleotides. The latter forms the most stable nucleosome yet characterized. One sequence with CAG repeats was also found. By fluorescence in situ hydridization the selected sequences are shown to be localized at the centromeric regions of mouse metaphase chromosomes.

Histone structure and the organization of the nucleosome

Chromatin structure is now believed to be dynamic and intimately related with cellular processes such as transcription. Over the past few years, high-resolution structures for the histones have become available. These structures and their implications for nucleosome organization are reviewed here.

A putative DNA binding surface in the globular domain of a linker histone is not essential for specific binding to the nucleosome

A fundamental step in the assembly of native chromatin is the specific recognition and binding of linker histones to the nucleoprotein subunit known as the nucleosome. A first step in defining this important interaction is the determination of residues within linker histones that are important for the structure-specific recognition of the nucleosome core. By combining in vitro assays for the native binding activity of linker histones and site-directed mutagenesis, we have examined a cluster of basic residues within the globular domain of H1(0), a somatic linker histone variant from Xenopus laevis. We show that these residues, which comprise a putative DNA binding surface within the globular domain, do not play an essential role in the structure-specific binding of a linker histone to the nucleosome.

Site-directed cleavage of DNA by a linker histone--Fe(II) EDTA conjugate: localization of a globular domain binding site within a nucleosome

The globular domain of linker histones specifically recognizes and binds to the nucleosome core. However, the exact location of the binding site of the globular domain has not been definitively elucidated. To address this issue, a linker histone has been specifically modified at a site adjacent to the globular domain with a radical-based DNA cleavage reagent. The linker histone-Fe(II) EDTA conjugate was bound to reconstituted nucleosomes containing a Xenopus 5S RNA gene, and the resulting cleavage of DNA was used to precisely map the location of the linker histone binding site. The results indicate that the binding site is located on the inside of the superhelical gyre of DNA, just inside the periphery of the nucleosome core region. The implications of these results for the binding of linker histones within native chromatin complexes are discussed.

Nucleosome disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis

We have examined the requirement for ATP in human (h) SWI/SNF-mediated alteration of nucleosome structure and facilitation of transcription factor binding to nucleosomal DNA. hSWI/SNF-mediated nucleosome alteration requires hydrolysis of ATP or dATP. The alteration is stable upon removal of ATP from the reaction or upon inhibition of activity by excess ATPgammaS, indicating that continued ATP hydrolysis is not required to maintain the altered nucleosome structure. This stable alteration is sufficient to facilitate binding of a transcriptional activator protein; concurrent ATP hydrolysis was not required to facilitate binding. These data suggest sequential steps that can occur in the process by which transcription factors gain access to nucleosomal DNA.

Nucleosome assembly on CTG triplet repeats

Expansion of CTG repeat sequences is associated with several human genetic diseases. We have examined the consequences of CTG repeat expansion for nucleosome assembly and positioning. Short CTG repeats are found within the most favored DNA sequences yet defined for nucleosome assembly. We find that as few as six CTG repeats will facilitate nucleosome assembly to a similar extent as the 50 or more repeats found in disease genes. Thus an increase in nucleosome stability on expansion of existing triplet repeats is unlikely to explain the acquisition of the disease phenotype. However, the CTG repeat sequence is efficiently wrapped around the histone octamer, preferring to associate with histones at the nucleosomal dyad. Thus short segments CTG repeat sequence will facilitate the assembly of a stable positioned nucleosome which might contribute to the expansion phenomenon and the functional organization of chromatin.

Nucleosome positioning properties of the albumin transcriptional enhancer

Considering the importance of nucleosome position with regard to how regulatory factors recognize their binding sites in chromatin, we have investigated the inherent nucleosome positioning properties of a transcriptional enhancer of the albumin gene. In the liver, where the albumin gene is highly expressed, the enhancer exists in an array of precisely positioned, nucleosome-like particles with transcription factors bound. In the absence of specific binding factors, such as in non-liver tissues or in polynucleosome arrays assembled in vitro, nucleosomes are randomly positioned over the enhancer. Herein we investigate the intrinsic nucleosome positioning properties of the central enhancer sequence assembled into mononucleosome core particles in vitro. We find that the enhancer DNA prefers three translational positions, each of which utilizes different rotational settings on the nucleosome core. We conclude that DNA binding factors that position nucleosomes may do so by stabilizing one configuration out of several that can be adopted by the underlying DNA, and that the potential exists for different positions to be stabilized at different stages of development.

Disruption of reconstituted nucleosomes. The effect of particle concentration, MgCl2 and KCl concentration, the histone tails, and temperature

We find that reconstituted nucleosome cores containing specific DNA sequences dissociate on dilution. This disruption of histone-DNA contacts leading to the release of free DNA is facilitated by the presence of the core histone tails, MgCl2 (5 mM), KCl (60 mM), and temperatures above 0 degree C. Under reaction conditions that are commonly used to assess trans-acting factor access to nucleosomal DNA, histone-DNA contacts are on the threshold of instability. We demonstrate how dilution of reconstituted nucleosomes containing a TATA box can facilitate TBP access to DNA.

Nucleosomes reconstituted in vitro on mouse mammary tumor virus B region DNA occupy multiple translational and rotational frames

The mouse mammary tumor virus acquires a highly reproducible chromatin structure when integrated into cellular DNA. Previous studies have suggested that the LTR is arranged as a series of six phased nucleosomes, that occupy specific positions on the LTR. On the basis of nucleosome reconstitution studies using DNA from the B region of the LTR, it has been argued that this sequence directs a uniquely positioned nucleosome. Here we demonstrate in vitro that reconstituted B region nucleosomes adopt at least five distinct translational positions in two rotational frames on a 206 bp fragment of DNA. We have resolved an initial reconstitute into its component species using nondenaturing gel electrophoresis, and precisely mapped the positions of each species using a hydroxyl radical footprinting assay. To confirm the nucleosome positions determined with the hydroxyl radical assay, nucleosome boundaries were mapped using exonuclease III. Comparison of the results from the hydroxyl radical footprinting and exonuclease III assays revealed a symmetrical pattern of overdigestion by exonuclease III which made unequivocal determination of nucleosome boundaries dubious. We conclude that the general use of exonuclease III to map the positions of nucleosomes may lead to incorrect assignment of position, and that assignment of position through the determination of the nucleosome pseudo-dyad from hydroxyl radical footprinting data represents a superior method of analysis.

Influence of dynamic fluctuations on DNA curvature

The effect of dynamic fluctuations on physical manifestations of DNA curvature such as electrophoretic retardation, circularization of DNA tracts and nucleosomes positioning is examined. It is shown that in all cases the main features of the processes can be satisfactorily explained by a static curvature model, which appears to be a good representation of time and ensemble averaged superstructures of DNA chains. The dynamic fluctuations around the average curvature appear to influence only the kinetics of these processes. In the case of polyacrylamide gel electrophoretic retardation it is demonstrated that the approximation of the static model holds on the assumption that dynamic fluctuations are independent from intrinsic curvature. The actual validity of the static model we proposed several years ago is satisfactorily demonstrated by the explanation and prediction of different experiments, such as cyclic permutation gel electrophoresis, differential DNAase I cleavage of cyclic versus linear DNA tracts and nucleosome positioning.

New insights into calicheamicin-DNA interactions derived from a model nucleosome system

Using the Xenopus borealis 5S RNA gene, we have identified several new features of the interaction of calicheamicin (CAL), an enediyne antitumor agent, with nucleosomal and naked DNA targets. CAL-mediated DNA damage was generally reduced by incorporation of the DNA into a nucleosome. However, in one instance, the frequency of DNA damage was enhanced in the nucleosome compared to naked DNA. This increase in CAL damage may result from bending-induced changes in the target site, while the association of histone proteins with DNA in the nucleosome may generally reduce the affinity of CAL for its targets by imposing dynamic constraints on the DNA, by altering target structure, or by steric hindrance. One implication of these observations is that new structural features created by incorporation of DNA into chromatin may produce 'hot spots' for CAL-mediated DNA damage not apparent in naked DNA studies. In a second set of experiments, the orientation of CAL at damage sites in naked 5S rDNA was determined. The results suggest that minor groove width per se is not a major determinant of CAL target selection. Our studies support the generality of an oligopurine recognition element, with the additional requirement that the purine tract is interrupted at the 3'-end by a pyrimidine(s). To account for these observations, we propose a model in which CAL recognizes the unique structural and dynamic features associated with the 3'-end of an oligopurine tract. Finally, we conclude that the dyad axis of pseudosymmetry of the 5S rRNA gene nucleosome cannot be determined with any degree of certainty. This places significant limitations on the interpretation of results from the study of drug-DNA interactions with reconstituted nucleosomes.

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.

Superstructural features of the upstream regulatory regions of two pea rbcS genes and nucleosomes positioning: theoretical prediction and experimental evaluation

Nucleosome positioning on two 384 bp DNA fragments, obtained from the upstream regulatory region of two pea rbcS genes, relevant in photoregulated transcription, was predicted using our theoretical method, based on the evaluation of the sequence dependent DNA bending energy. The theoretical prediction was checked by experimental evaluation of nucleosome positions after in vitro reconstitution, by mapping Exonuclease III-resistant borders and by digesting monomeric sequences with various restriction enzymes. Both approaches satisfactorily confirmed the theoretical predictions, showing that the nucleotide sequence intrinsic bendability has a dominant role in nucleosome positioning.

DNA structural patterns and nucleosome positioning

There is no clear picture to date of the mechanisms determining nucleosome positioning. Generally, local DNA sequence signals (sequence-dependent positioning) or non-local signals (e.g. boundary effects) are possible. We have analyzed the DNA sequences of a series of positioned and mapped nucleosome cores in a systematic search for local sequence signals. The data set consists of 113 mapped nucleosome cores, mapped in vivo, in situ, or in reconstituted chromatin. The analysis focuses on the periodic distribution of sequence elements implied by each of six different published DNA structural models. We have also investigated the periodic distribution of all mono-, di-, and trinucleotides. An identical analysis was performed on a set of isolated chicken nucleosome cores (nucleosome data from the literature) that are presumably positioned due to local sequence signals. The results show that the sequences of the isolated nucleosome cores have a number of characteristic features that distinguish them clearly from randomly chosen reference DNA. This confirms that the positioning of these nucleosomes is mainly sequence-dependent (i.e., dependent on local octamer-DNA interactions) and that our algorithms are able to detect these patterns. Using the same algorithms, the sequences of the mapped nucleosome cores, however, are on average very similar to randomly chosen reference DNA. This suggests that the position of the majority of these nucleosomes can not be attributed to the sequence patterns implemented in our algorithms. The arrangement of positioned nucleosomes seems to be the result of a dynamic interplay of octamer-DNA interactions, nucleosome-nucleosome interactions and other positioning signals with varying relative contributions along the DNA.

Structure of DNA in a nucleosome core at high salt concentration and at high temperature

We have used hydroxyl radical cleavage of DNA to probe the organization of the nucleosome core at high salt concentration and high temperature. The rotational and translational positioning of a DNA fragment, containing part of the Xenopus borealis 5S RNA gene, on the histone octamer is maintained between salt concentrations of 0.0 and 0.8 M NaCl and between temperatures of 0 and 75 degrees C. These results provide evidence that the energy of bending DNA around the nucleosome is independent of salt concentration and temperature in this range. They illustrate the severe energetic requirements necessary to displace DNA from previously organized contacts with histones in the nucleosome core.

In vitro binding to the leucine tRNA gene identifies a novel yeast homeobox gene

In a search for gene products of Saccharomyces cerevisiae interacting with the internal promoter of yeast tRNA genes two genes encoding a homeodomain protein of the Drosophila Antennapedia type were isolated. One of them codes for Pho2, and the second codes for a previously unknown protein (Yox1). The corresponding gene, termed YOX1, maps to chromosome 16. The amino acid sequence of Yox1 shows a remarkable similarity within the homeobox domain to many proteins from a wide variety of sources. Fusion proteins that contain sequences encoded by these genes demonstrate that the genes encode DNA-binding proteins that are capable of binding to the DNA of the leucine tRNA gene in vitro. However, deletion of YOX1 gene activity does not give rise to a scorable mutant phenotype. This result leaves open whether Yox1 binding to the leucine tRNA gene is necessary for the in vivo regulation of the gene and its suggests that the YOX1 gene codes for a non-essential product.

A positive role for histone acetylation in transcription factor access to nucleosomal DNA

Acetylation of the N-terminal tails of the core histones directly facilitates the recognition by TFIIIA of the 5S RNA gene within model chromatin templates. This effect is independent of a reduction in the extent of histone-DNA interactions or a change in DNA helical repeat; it is also independent of whether a histone tetramer or octamer inhibits TFIIIA binding. Removal of the N-terminal tails from the core histones also facilitates the association of TFIIIA with nucleosomal templates. We suggest that the histone tails have a major role in restricting transcription factor access to DNA and that their acetylation releases this restriction by directing dissociation of the tails from DNA and/or inducing a change in DNA configuration on the histone core to allow transcription factor binding. Acetylation of core histones might be expected to exert a major influence on the accessibility of chromatin to regulatory molecules.

A nucleosome core is transferred out of the path of a transcribing polymerase

We have determined the fate of a nucleosome core on transcription. A nucleosome core was assembled on a short DNA fragment and ligated into a plasmid containing a promoter and terminators for SP6 RNA polymerase. The nucleosome core was stable in the absence of transcription. The distribution of nucleosome cores after transcription was examined. The histone octamer was displaced from its original site and reformed a nucleosome core at a new site within the same plasmid molecule, with some preference for the untranscribed region behind the promoter. These observations eliminate several models that have been proposed for transcription through a nucleosome core. Our results suggest that a nucleosome core in the path of a transcribing polymerase is displaced by transfer to the closest acceptor DNA.

Modulation of progesterone receptor binding to progesterone response elements by positioned nucleosomes

In cells, steroid hormone receptors interact with target enhancer elements on nucleosomes to regulate transcription of genes. To elucidate how nucleosomes can potentially regulate the interactions of steroid receptors with steroid response elements, we have examined the effects of nucleosome positioning and histone source on the binding of the progesterone receptor to DNA elements on nucleosomes reconstituted in vitro. We find that the affinity of the receptor for its response element is dependent on the position of the element within the nucleosome, but not on the histone source, active or inactive chromatin. Our results suggest that the strength of DNA-histone interactions within the nucleosome modulates the binding of progesterone receptor to response elements. Thus, nucleosome positioning is likely to influence the function of steroid receptors in vivo.

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.

Mobility of positioned nucleosomes on 5 S rDNA

We report on a dynamic aspect of nucleosome positioning, in the absence of transcription-related events, on sea urchin 5 S rDNA. On tandem repeats of nucleosome length DNA of this strongly positioning sequence, histone octamers assemble in one dominant position surrounded by minor positions, ten base-pairs apart and therefore with identical rotational setting of the DNA coil. The existence of this cluster of positions, determined using micrococcal nuclease is confirmed by the results from DNase I footprinting and restriction enzyme analysis. The results from these techniques and from two-dimensional nucleoprotein polyacrylamide gel analysis indicate that the cluster of octamer positions is in dynamic equilibrium, in low ionic conditions, suggesting that the minor positions reflect fluctuations around the major nucleosome site. Histone octamer mobility appears to be temperature dependent and is reversibly inhibited by Mg2+.

Sequence-specific binding of the N-terminal three-finger fragment of Xenopus transcription factor IIIA to the internal control region of a 5S RNA gene

An N-terminal fragment of Xenopus TFIIIA, containing domains 1-3, (TF 3), was expressed in E. coli. High yields of recombinant zinc finger protein was isolated, and its DNA binding activity for the internal control region (ICR) of the Xenopus 5S RNA gene, was demonstrated by band-shift experiments and DNase I footprinting analysis. TF 3 protects 20 bp of ICR against DNase I digestion. The limits of protection are from +77 to +96 on both coding and noncoding strand. This protection pattern is identical to the protection pattern obtained with TFIIIA in the overlapping region, showing that the 3-finger fragment accounts fully for the protein-DNA interactions in TFIIIA-5S RNA gene over this region.

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.

The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning

Using our model for predicting DNA superstructures from the sequence, the average distribution of the phases of curvature along the sequences of the set of the 177 nucleosomal DNAs investigated by Satchwell et al. (J. Mol. Biol. 191 (1986) 659) was calculated. The diagram obtained shows very significant features which allow the visualization of the intrinsic nucleosomal superstructure characterized by two quasi-parallel tracts of a flat left-handed superhelical turn connected by a left-handed inflection in a perpendicular direction; such a superstructure appears to be closely related to the nucleosome model of Travers and Klug (Phil. Trans. R. Soc. Lond. 317 (1987) 537). The nucleosomal curvature phase diagram was then adopted as a sensitive determinant for the nucleosome virtual positioning in DNAs via correlation function, obtaining a good agreement with the experimental mapping of SV40 regulatory region as recently investigated by Ambrose et al. (J. Mol. Biol. 209 (1989) 255). This analysis shows also the presence of a constant phase relation between the virtual nucleosome positions which suggests its possible implication in the nucleosome condensation in chromatin.

Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter

Minichromosomes containing the MMTV hormone responsive element (HRE) exhibit precisely positioned nucleosomes. Chromatin reconstitution of short HRE DNA fragments also results in precise positioning of nucleosomes as revealed by footprinting, which suggests that information for nucleosome phasing is contained within this short sequence. While hormone receptors bind naked DNA and reconstituted nucleosomes with similar affinities (3- to 5-fold difference), NFI, a transcription factor essential for efficient utilization of the MMTV promoter, binds naked DNA very tightly but does not bind the nucleosomally organized promoter. Hormone receptor binding to the MMTV nucleosome does not dissociate the nucleosome but leads to greater accessibility of the promoter-proximal end to exonuclease III. Precise positioning of one nucleosome over the MMTV promoter could repress transcription by preventing NFI binding in the absence of hormone, while still allowing interaction of activated hormone receptor with HRE.

Nucleosome positioning can affect the function of a cis-acting DNA element in vivo

Positioning of nucleosomes has been proposed as one mechanism whereby the activity of DNA is regulated: cis-acting elements located in linker DNA might be more accessible for interaction with trans-acting protein factors than they would be if they were directly associated with histones in nucleosome core particles. The eleven base pairs constituting the autonomously replicating sequence (ARS) of the high-copy-number TRP1ARS1 plasmid of Saccharomyces cerevisiae are located in a linker region near the edge of a positioned nucleosome and form an origin of replication. Could nucleosome positioning render the ARS accessible for interaction with the proteins necessary for its function? I have tested this hypothesis by making deletions and an insertion to move the ARS into the nucleosome DNA and then examining the effects on ARS function. There is a marked decrease in copy number when the ARS is moved into the central DNA region of the nucleosome core particle, a region known to differ in structure and stability from the peripheral segments of nucleosome DNA.