The transcriptionally-active MMTV promoter is depleted of histone H1

How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry

Molecular dynamics simulations have been employed to determine the optimal conformation of an estrogen receptor DNA binding domain dimer bound to a consensus response element, ds(AGGTCACAGTGACCT), and to a nonconsensus response element, ds(AGAACACAGTGACCT). The structures simulated were derived from a crystallographic structure and solvated by a sphere (45-A radius) of explicit water and counterions. Long-range electrostatic interactions were accounted for during 100-ps simulations by means of a fast multipole expansion algorithm combined with a multiple time-step scheme in the molecular dynamics package NAMD. The simulations demonstrate that the dimer induces a bent and underwound (10.7 bp/turn) conformation in the DNA. The bending reflects the dyad symmetry of the receptor dimer and can be described as an S-shaped curve in the helical axis of DNA when projected onto a plane. A similar bent and underwound conformation is observed for nucleosomal DNA near the nucleosome's dyad axis that reflects the symmetry of the histone octamer. We propose that when a receptor dimer binds to a nucleosome, the most favorable dimer-DNA and histone-DNA interactions are achieved if the respective symmetry axes are aligned. Such positioning of a receptor dimer over the dyad of nucleosome B in the mouse mammary tumor virus promoter is in agreement with experiment.

Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer

To investigate mechanisms yielding DNase I-hypersensitive sites (DHSs) at gene regulatory regions, we have initiated a biochemical analysis of transcription factor binding and nucleosome remodeling with a region of the human immunodeficiency virus 1 (HIV-1) 5' long terminal repeat (LTR) that harbors constitutive DHSs in vivo. In vitro reconstitution of an HIV-1 5' LTR fragment into nucleosome core particles demonstrates that Sp1, NF-kappaB1, LEF-1, ETS-1 and USF can gain access to their binding sites in HIV-1 nucleosomal DNA. The factor-bound mononucleosomes resist histone displacement from the DNA by the chromatin remodeling activity, SW1-SNF, or the histone chaperone, nucleoplasmin, suggesting that the binding of these factors to nucleosomal HIV-1 sequences forms a stable complex that includes the underlying histones. However, when the HIV-1 5' LTR fragment is incorporated into a nucleosomal array, Sp1 and NF-kappaB1 binding produce regions of enhanced DNase I sensitivity specifically at the HIV-1 nucleosome. These regions resemble the observed in vivo DHSs, yet the HIV-1 nucleosome remains intact even in the presence of nucleoplasmin. Thus, the constitutive DHSs identified at the HIV-1 enhancer in native chromatin may reflect the presence of a ternary complex composed of transcriptional activators, histones and DNA.

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.

Analysis of chromatin structure in vivo

A number of important nuclear processes including replication, recombination, repair, and transcription involve the interaction of soluble nuclear proteins with DNA assembled as chromatin. Recent progress in a number of experimental systems has focused attention on the influence chromatin structure may exert on gene regulation in eukaryotes. With the advent of new technologies for the analysis of chromatin structure in vivo, studies evaluating the influence of chromatin structure on gene transcription have become feasible for a number of systems. This article serves as an introduction to the use of restriction endonucleases to define nucleosomal organization and characterize changes in this organization that accompany transcriptional activation in vivo. The procedure includes the isolation of intact transcriptionally competent nuclei, limited digestion with specific restriction endonucleases, and purification of the DNA. This DNA serves as the substrate for a linear amplification using single primers that generate enzyme-specific DNA fragments, which are then resolved by electrophoresis. Specific examples related to our studies of the influence of chromatin structure on steroid hormone regulation of transcription from the mouse mammary tumor virus promoter are provided to illustrate this technique and several novel variations. Alternative methods for analysis of chromatin architecture using DNase I, micrococcal nuclease, permanganate, and methidiumpropyl-EDTA-iron(II) are also described. Through the use of these methodologies one is able to determine both the translational and the rotational positions for a given nucleosome as well as quantify changes at a specific nucleosome in response to regulatory and developmental signals.

Synergism between hypersensitive sites confers long-range gene activation by the beta-globin locus control region

The human beta-globin locus control region (LCR) consists of four erythroid-specific DNaseI hypersensitive sites (HSs) at the 5' end of the beta-globin cluster. The LCR functions over a long distance on chromosome 11 to regulate transcription and replication of the beta-globin genes. To determine whether the HSs function independently or as an integrated unit, we analyzed the requirements for long-range transcriptional activation. If the HSs function independently, individual HSs would be expected to have long-range activity. In contrast, if long-range activity requires multiple HSs, individual HSs would have a limited functional distance. HS2, HS3, and a miniLCR containing multiple HSs, were separated from a gamma-globin promoter by fragments of phage lambda DNA. After stable transfection into K562 cells, HS2 had strong enhancer activity, but only when positioned close to the promoter. HS3 also had strong enhancer activity, although it was weaker than HS2 and more sensitive to the spacer DNA. The miniLCR had the strongest enhancer activity and functioned even at a distance of 7.3 kb. A model is proposed in which synergistic interactions between HSs confer long-range activation by creating a stable LCR nucleoprotein structure, which is competent for recruiting chromatin-modifying enzymes. These enzymes would mediate the well-characterized activity of the LCR to modulate chromatin structure.

Remodeling chromatin structures for transcription: what happens to the histones?

Activation of gene transcription in vivo is accompanied by an alteration of chromatin structure. The specific binding of transcriptional activators disrupts nucleosomal arrays, suggesting that the primary steps leading to transcriptional initiation involve interactions between activators and chromatin. The affinity of transcription factors for nucleosomal DNA is determined by the location of recognition sequences within nucleosomes, and by the cooperative interactions of multiple proteins targeting binding sites contained within the same nucleosomes. In addition, two distinct types of enzymatic complexes facilitate binding of transcription factors to nucleosomal DNA. These include type A histone acetyltransferases (e.g. GCN5/ADA transcriptional adaptor complex) and ATP-driven molecular machines that disrupt histone-DNA interactions (e.g. SWI/SNF and NURF complexes). These observations raise the important question of what happens to the histones during chromatin remodeling. We discuss evidence supporting the retention of histones at transcription factor-bound sequences as well as two alternative pathways of histone loss from gene control elements upon transcription factor binding: histone octamer sliding and histone dissociation.

An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres

Histone-DNA contacts within a nucleosome influence the function of trans-acting factors and the molecular machines required to activate the transcription process. The internal architecture of a positioned nucleosome has now been probed with the use of photoactivatable cross-linking reagents to determine the placement of histones along the DNA molecule. A model for the nucleosome is proposed in which the winged-helix domain of the linker histone is asymmetrically located inside the gyres of DNA that also wrap around the core histones. This domain extends the path of the protein superhelix to one side of the core particle.

NF-E2 disrupts chromatin structure at human beta-globin locus control region hypersensitive site 2 in vitro

The human beta-globin locus control region (LCR) is responsible for forming an active chromatin structure extending over the 100-kb locus, allowing expression of the beta-globin gene family. The LCR consists of four erythroid-cell-specific DNase I hypersensitive sites (HS1 to -4). DNase I hypersensitive sites are thought to represent nucleosome-free regions of DNA which are bound by trans-acting factors. Of the four hypersensitive sites only HS2 acts as a transcriptional enhancer. In this study, we examine the binding of an erythroid protein to its site within HS2 in chromatin in vitro. NF-E2 is a transcriptional activator consisting of two subunits, the hematopoietic cell-specific p45 and the ubiquitous DNA-binding subunit, p18. NF-E2 binds two tandem AP1-like sites in HS2 which form the core of its enhancer activity. In this study, we show that when bound to in vitro-reconstituted chromatin, NF-E2 forms a DNase I hypersensitive site at HS2 similar to the site observed in vivo. Moreover, NF-E2 binding in vitro results in a disruption of nucleosome structure which can be detected 200 bp away. Although NF-E2 can disrupt nucleosomes when added to preformed chromatin, the disruption is more pronounced when NF-E2 is added to DNA prior to chromatin assembly. Interestingly, the hematopoietic cell-specific subunit, p45, is necessary for binding to chromatin but not to naked DNA. Interaction of NF-E2 with its site in chromatin-reconstituted HS2 allows a second erythroid factor, GATA-1, to bind its nearby sites. Lastly, nucleosome disruption by NF-E2 is an ATP-dependent process, suggesting the involvement of energy-dependent nucleosome remodeling factors.

Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones

To investigate mechanisms of chromatin remodeling, we have examined the fate of a single nucleosome core within a spaced nucleosome array upon the binding of transcription factors. GAL4 binding to this nucleosome within an array resulted in the establishment of DNase I hypersensitivity adjacent to the bound factors mimicking in vivo hypersensitive sites. The positions of adjacent nucleosomes were unchanged upon GAL4 binding, suggesting that histone octamer sliding did not occur. In addition, novel assays were used to determine whether the histones remained present during factor binding. GAL4 binding alone did not independently dislodge or move the underlying histones, which remained in a ternary complex with the bound GAL4. GAL4 binding did, however, specifically predispose the histones contained in this nucleosome to displacement in trans. Addition of the histone binding protein, nucleoplasmin, mediated the displacement of the core histones in the GAL4-bound nucleosome, resulting in the formation of a nucleosome-free region. These data illustrate trans-displacement of histones as one mechanism for transcription factor-targeted generation of a nucleosome-free region in chromatin. They also illustrate the limitations of nuclease digestions in analyzing changes in chromatin structure and provide important mechanistic details beyond the basic phenomenon of DNase I hypersensitivity.

Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex

The SWI/SNF complex participates in the restructuring of chromatin for transcription. The function of the yeast SWI/SNF complex in the remodeling of a nucleosome array has now been analyzed in vitro. Binding of the purified SWI/SNF complex to a nucleosome array disrupted multiple nucleosomes in an adenosine triphosphate-dependent reaction. However, removal of SWI/SNF left a deoxyribonuclease I-hypersensitive site specifically at a nucleosome that was bound by derivatives of the transcription factor Gal4p. Analysis of individual nucleosomes revealed that the SWI/SNF complex catalyzed eviction of histones from the Gal4-bound nucleosomes. Thus, the transient action of the SWI/SNF complex facilitated irreversible disruption of transcription factor-bound nucleosomes.

Either of the major H2A genes but not an evolutionarily conserved H2A.F/Z variant of Tetrahymena thermophila can function as the sole H2A gene in the yeast Saccharomyces cerevisiae

H2A.F/Z histones are conserved variants that diverged from major H2A proteins early in evolution, suggesting they perform an important function distinct from major H2A proteins. Antisera specific for hv1, the H2A.F/Z variant of the ciliated protozoan Tetrahymena thermophila, cross-react with proteins from Saccharomyces cerevisiae. However, no H2A.F/Z variant has been reported in this budding yeast species. We sought to distinguish among three explanations for these observations: (i) that S. cerevisiae has an undiscovered H2A.F/Z variant, (ii) that the major S. cerevisiae H2A proteins are functionally equivalent to H2A.F/Z variants, or (iii) that the conserved epitope is found on a non-H2A molecule. Repeated attempts to clone an S. cerevisiae hv1 homolog only resulted in the cloning of the known H2A genes yHTA1 and yHTA2. To test for functional relatedness, we attempted to rescue strains lacking the yeast H2A genes with either the Tetrahymena major H2A genes (tHTA1 or tHTA2) or the gene (tHTA3) encoding hv1. Although they differ considerably in sequence from the yeast H2A genes, the major Tetrahymena H2A genes can provide the essential functions of H2A in yeast cells, the first such case of trans-species complementation of histone function. The Tetrahymena H2A genes confer a cold-sensitive phenotype. Although expressed at high levels and transported to the nucleus, hv1 cannot replace yeast H2A proteins. Proteins from S. cerevisiae strains lacking yeast H2A genes fail to cross-react with anti-hv1 antibodies. These studies make it likely that S. cerevisiae differs from most other eukaryotes in that it does not have an H2A.F/Z homolog. A hypothesis is presented relating the absence of H2A.F/Z in S. cerevisiae to its function in other organisms.

Phosphorylation/dephosphorylation of the repressor MDBP-2-H1 selectively affects the level of transcription from a methylated promoter in vitro

We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogenin II gene, we optimised an in vitro transcription system using HeLa nuclear extracts. We show that in the absence of the phosphorylated form of MDBP-2-H1 from rooster, methylation of the vitellogenin II promoter does not affect the transcription. Addition of purified MDBP-2-H1 from rooster to the in vitro transcription system inhibits transcription more efficiently from a methylated than an unmethylated DNA template. Dephosphorylation of rooster MDBP-2-H1 by phosphatase treatment or estradiol treatment of rooster lead to the loss of inhibitory activity of the protein when added to the in vitro transcription assays. These findings indicate that the phosphorylation of MDBP-2-H1 is essential for the repression of the transcription. Taken together these results establish the relationship between the dephosphorylation of MDBP-2-H1 caused by estradiol, the down regulation of its binding activity to methylated DNA and the derepression of vitellogenin II transcription.

Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site

DNase I-hypersensitive sites lack a canonical nucleosome and have binding sites for various transcription factors. To understand how the hypersensitivity is generated and maintained, we studied the chicken erythroid-specific beta(A)/epsilon globin gene enhancer, a region where both tissue-specific and ubiquitous transcription factors can bind. Constructions containing mutations of this enhancer were stably introduced into a chicken erythroid cell line. We found that the hypersensitivity was determined primarily by the erythroid factors and that their binding additively increased the accessibility. The fraction of accessible sites in clonal cell lines was quantitated using restriction endonucleases; these data implied that the formation of each hypersensitive site was an all-or-none phenomenon. Use of DNase I and micrococcal nuclease probes further indicated that the size of the hypersensitive site was influenced by the binding of transcription factors which then determined the length of the nucleosome-free gap. Our data are consistent with a model in which hypersensitive sites are generated stochastically: mutations that reduce the number of bound factors reduce the probability that these factors will prevail over a nucleosome; thus, the fraction of sites in the population that are accessible is also diminished.

Pushing nucleosomes around. Chromatin

Nucleosomes assembled on regulatory DNA sites in chromatin repress gene expression; protein factors have now been identified that can help overcome such repression by excluding or remodelling nucleosomes so regulatory sites are accessible to transcription factors.

Repression and activation by multiprotein complexes that alter chromatin structure

Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

Regulation of gene expression by nucleosomes

During the past year, the characterization of mechanisms and factors capable of disrupting nucleosomes during transcriptional activation has been a recurrent theme in studies which address the contribution of nucleosome structure to gene regulation. In vivo studies using yeast and Drosophila together with biochemical purification schemes using nucleosome perturbation assays have provided evidence for the existence of multiprotein complexes that are able to alleviate nucleosome repression. At the same time, new insights into the mechanism of heterochromatin formation have been gained, which have direct links to nucleosome structure.

Transcription factors and the cardiac gene programme

During the past decade, major advances have been made in uncovering the mechanisms that switch genes on and off. Gene methylation and histones play an important role in gene (in)activation. Following gene activation, the initiation of transcription by RNA polymerase requires the assembly of multiple protein complexes on the promoter region of a gene. How a cell type-specific gene expression pattern can be induced is a key question in cardiovascular biology today. Members of the helix-loop-helix-family of the transcription factors play a dominant role in skeletal muscle formation. In cardiac muscle the situation is less obvious. Recent studies identified muscle transcription factors like MEF-2, TEF-1 and MNF, which are common to both the skeletal and cardiac muscle lineages. A few transcription factors, among which Nkx 2.5 and GATA-4, are expressed predominantly in the heart. The absence of master regulators in the heart points to the importance of interaction between ubiquitous factors and tissue restricted factors to initiate the cardiac gene programme and to lock these cells in their differentiated state. The recent development of murine transgenic and gene-targeting technology provides tools to study the role of mammalian transcription factors in vivo. Interesting cardiac phenotypes are found in gene targeted mice, indicating a crucial role for retinoic acid and homeobox genes in murine cardiogenesis.

Transcriptional regulation by steroid hormones

Steroid hormones influence the transcription of a large number of genes by virtue of their interaction with intracellular receptors, which are modular proteins composed of a ligand binding domain, a DNA binding domain, and several transactivation functions distributed along the molecule. The DNA binding domain is organized around two zinc ions and allows the receptors to bind as homodimers to palindromic DNA sequences, the hormones responsive elements (HRE), is such a way that each homodimer contacts one half of the palindrome. Since the two halves are separated by three base pairs, the two homodimers contact the same face of the double helix. Before hormone binding, the receptors are part of a complex with multiple chaperones which maintain the receptor in its steroid binding conformation. Following hormone binding, the complex dissociates and the receptors bind to HREs in chromatin. Regulation of gene expression by hormones involves an interaction of the DNA-bound receptors with other sequence-specific transcription factors and with the general transcription factors, which is partly mediated by co-activators and co-repressors. The specific array of cis regulatory elements in a particular promoter/enhancer region, as well as the organization of the DNA sequences in nucleosomes, specifies the network of receptor interactions. Depending on the nature of these interactions, the final outcome can be induction or repression of transcription. The various levels at which these interactions are modulated are discussed using as an example the promoter of the Mouse Mammary Tumor Virus and its organization in chromatin.

Chromatin structure of the MMTV promoter and its changes during hormonal induction

1. The packaging of nuclear DNA in chromatin determines the conversion of the genetic information into a defined phenotype by influencing the availability of DNA sequences for interactions with regulatory proteins and transcription factors. 2. We have studied the influence of the first level of chromatin organization, the nucleosome, on the activity of the mouse mammary tumor virus (MMTV) promoter. The MMTV promoter is strongly transcribed in response to steroid hormones but is virtually silent in the absence of hormonal stimuli. Full hormonal induction requires binding of the hormone receptors to four hormone-responsive elements (HREs), as well as binding of nuclear factor I (NFI) and the octamer transcription factor 1 (OTF-1 or Oct-1) to sites located between the HREs and the TATA box. A full loading with transcription factors cannot be achieved on free DNA due to steric hindrance between hormone receptor and NFI and between NFI and OTF-1. 3. The low basal activity of the MMTV promoter is most likely due to its organization in a positioned nucleosome. In the intact cell, as well in reconstituted chromatin, the regulatory region of the MMTV promoter is wrapped around a histone octamer in a precise rotational orientation, which permits access of the hormone receptors to only two of the four HREs, while precluding binding of NFI and OTF-1 to their respective sites. Upon hormone induction, the nucleosome is remodeled and the path of its DNA altered in a way which makes the nucleosomal dyad axis more accessible to DNase I and enables occupancy of all relevant sites: the four HREs, as well as the binding sites for NFI and OTF-1. 4. These results suggest that the nucleosomal organization of the MMTV promoter not only is responsible for the low activity prior to hormone treatment, but also may be a prerequisite for full loading with transcription factors after hormone induction. We conclude that the DNA contains topological information which modulates the expression of the genetic program.

Direct activation and anti-repression functions of GAL4-VP16 use distinct molecular mechanisms

In order to determine whether the molecular mechanisms used for direct activation by GAL4-VP16 are the same as those used for anti-repression, we have employed monoclonal antibodies specific for the VP16 activation domain. In the absence of added repressors, GAL4-VP16 was able to stimulate transcription from a template containing GAL4-binding sites, and the antibodies raised against the VP16 activation domain failed to inhibit this direct activation. GAL4-VP16 also was able to prevent histone H1-mediated repression by a mechanism that was strongly dependent on the presence of specific GAL4-binding elements in the promoter. However, in contrast to the assays conducted in the absence of repressors, the antibodies were strong inhibitors of GAL4-VP16-activated transcription in the presence of histone H1. Thus the binding of the antibodies distinguished between the direct activation and anti-repression functions of GAL4-VP16, indicating that these functions operate through distinct molecular mechanisms. The anti-repression-specific mechanism that is inhibitable by the antibodies acted at an early stage of preinitiation complex formation. Deletions of individual subdomains of the VP16 activation domain demonstrated that there was not a discrete subdomain responsible for the anti-repression function of GAL4-VP16. Thus, the inhibitory effect of the antibodies appeared to be due to the location of the epitope within the activator protein rather than to some inherent biochemical property of that region of the protein that is required specifically for anti-repression. The inhibitory effect of the antibodies also ruled out the possibility that steric exclusion of repressor proteins from the promoter was the sole means of anti-repression by the transcriptional activator.

Constitutive repression and nuclear factor I-dependent hormone activation of the mouse mammary tumor virus promoter in Saccharomyces cerevisiae

To study the influence of various transactivators and the role of nucleosomal structure in gene regulation by steroid hormones, we have introduced mouse mammary tumor virus (MMTV) promoter sequences along with expression vectors for the glucocorticoid receptor (GR) and nuclear factor I (NFI) in Saccharomyces cerevisiae, an organism amenable to genetic manipulation. Both in the context of an episomal multicopy vector and in a centromeric single-copy plasmid, the MMTV promoter was virtually silent in the absence of inducer, even in yeast strains expressing GR and NFI. Induction was optimal with deacylcortivazol and required both GR and NFI. The transactivation function AF1 in the N-terminal half of GR is required for ligand-dependent induction and acts constitutively in truncated GR lacking the ligand binding domain. A piece of the MMTV long terminal repeat extending from -236 to +111 is sufficient to position a nucleosome, B, over the regulatory region of the promoter from -45 to -190 and another nucleosome over the transcription start region. The rotational orientation of the DNA on the surface of nucleosome B is the same as that previously found in animal cells and in reconstitution experiments. This orientation is compatible with binding of GR to two sites, while it should preclude binding of NFI and hence be responsible for constitutive repression. Upon ligand induction, there is no major chromatin rearrangement, but the proximal linker DNA, including the TATA box, becomes hypersensitive to nucleases. The transcriptional behavior of the MMTV promoter was unaffected by deletions of the genes for zuotin or SIN1/SPT2, two proteins which have been claimed to assume some of the functions of linker histones. Thus, despite the lack of histone H1, yeast cells could be a suitable system to study the contribution of nucleosomal organization to the regulated expression of the MMTV promoter.

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.

Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames

The translational positions of nucleosomes in the promoter region of the mouse mammary tumor virus (MMTV) were defined at high resolution. Nucleosome boundaries were determined in primer extension assays using full-length single-stranded mononucleosomal DNA prepared from cells treated with formaldehyde, a reversible protein-DNA cross-linking agent. Multiple boundaries were observed in both the nucleosome A (Nuc-A) and Nuc-B region of the promoter, indicating multiple nucleosome translational frames. The different nucleosome frames in both the Nuc-A and Nuc-B regions were occupied unequally. The most frequently occupied frames were found clustered within 50-60 bases of each other, resulting in a distribution centered in the positions defined previously at low resolution for Nuc-A and Nuc-B. The most abundant 5' ends of the frames in the B region were found between -235 and -187, and the 3' ends between -86 and -36, whereas in the A region the most abundant 5' ends were between -22 and +42, and the 3' ends between +121 and +186. Although frames in the Nuc-B region of the LTR extend at a low frequency in the 5' direction toward the Nuc-C region, there is a sharp discontinuity in the 3' direction toward Nuc-A, suggesting the presence of a boundary constraint in the A-B linker. The positions and relative occupancies of nucleosome frames, in either the B or the A region, did not change when the promoter was activated with dexamethasone.

Nucleoprotein structure influences the response of the mouse mammary tumor virus promoter to activation of the cyclic AMP signalling pathway

Recent studies have provided evidence of crosstalk between steroid receptors and cyclic AMP (cAMP) signalling pathways in the regulation of gene expression. A synergism between intracellular phosphorylation inducers and either glucocorticoids or progestins has been shown to occur during activation of the mouse mammary tumor virus (MMTV) promoter. We have investigated the effect of 8-Br-cAMP and okadaic acid, modulators of cellular kinases and phosphatases, on the hormone-induced activation of the MMTV promoter in two forms: a transiently transfected template with a disorganized, accessible nucleoprotein structure and a stably replicating template with an ordered, inaccessible nucleoprotein structure. Both okadaic acid and 8-Br-cAMP synergize significantly with either glucocorticoids or progestins in activating the transiently transfected MMTV template. In contrast, 8-Br-cAMP, but not okadaic acid, is antagonistic to hormone-induced activation of the stably replicating MMTV template. Nuclear run-on experiments demonstrate that this inhibition is a transcriptional effect on both hormone-induced transcription and basal transcription. Surprisingly, 8-Br-cAMP does not inhibit glucocorticoid-induced changes in restriction enzyme access and nuclear factor 1 binding. However, association of a complex with the TATA box region is inhibited in the presence of 8-Br-cAMP. Thus, cAMP treatment interferes with the initiation process but does not inhibit interaction of the receptor with the template. Since the replicated, ordered MMTV templates and the transfected, disorganized templates show opposite responses to 8-Br-cAMP treatment, we conclude that chromatin structure can influence the response of a promoter to activation of the cAMP signalling pathway.

Deposition of histone H1 onto reconstituted nucleosome arrays inhibits both initiation and elongation of transcripts by T7 RNA polymerase

The effect of histone H1 on transcription by bacteriophage T7 RNA polymerase was examined using reconstituted chromatin templates. A 3.8 kb linear DNA template consisting of a specific transcription promoter for T7 RNA polymerase placed upstream of 18 tandem repeats of a 207 bp nucleosome positioning sequence derived from the 5S rRNA gene of Lytechinus variegatus was used as a template for chromatin reconstitution. Regularly spaced arrays of nucleosome cores were assembled onto this DNA template from donor histone octamers by salt step dialysis. Histone H1 was incorporated onto free DNA or reconstituted chromatin templates and double label transcription assays were performed. The experiments indicated that histone H1 has a strong inhibitory effect on both transcription initiation and elongation. These effects are especially pronounced on chromatin templates, where both transcription initiation and elongation are virtually halted. The inhibition of transcription elongation appears to result from a dramatic increase in premature termination of transcripts. These experiments indicate that assembly of histone H1 into chromatin can result in structures which are completely repressed with respect to transcription.

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

To investigate mechanisms by which multiple transcription factors access complex promoters and enhancers within cellular chromatin, we have analyzed the binding of disparate factors to nucleosome cores. We used a purified in vitro system to analyze binding of four activator proteins, two GAL4 derivatives, USF, and NF-kappa B (KBF1), to reconstituted nucleosome cores containing different combinations of binding sites. Here we show that binding of any two or all three of these factors to nucleosomal DNA is inherently cooperative. Thus, the binuclear Zn clusters of GAL4, the helix-loop-helix/basic domains of USF, and the rel domain of NF-kappa B all participated in cooperative nucleosome binding, illustrating that this effect is not restricted to a particular DNA-binding domain. Simultaneous binding by two factors increased the affinity of individual factors for nucleosomal DNA by up to 2 orders of magnitude. Importantly, cooperative binding resulted in efficient nucleosome binding by factors (USF and NF-kappa B) which independently possess little nucleosome-binding ability. The participation of GAL4 derivatives in cooperative nucleosome binding required only DNA-binding and dimerization domains, indicating that disruption of histone-DNA contacts by factor binding was responsible for the increased affinity of additional factors. Cooperative nucleosome binding required sequence-specific binding of all transcription factors, appeared to have spatial constraints, and was independent of the orientation of the binding sites on the nucleosome. These results indicate that cooperative nucleosome binding is a general mechanism that may play a significant role in loading complex enhancer and promoter elements with multiple diverse factors in chromatin and contribute to the generation of threshold responses and transcriptional synergy by multiple activator sites in vivo.

The effect of histone H1 and DNA methylation on transcription

We have previously shown that DNA methylation acts as a focus for the formation of inactive chromatin in vivo. We have investigated the mechanism further by in vitro transcription of a template containing two tRNA genes and an extensive (G+C)-rich sequence characteristic of a CpG island. The extent of transcription from the unmethylated or fully methylated template was assayed in the presence of varied levels of histone H1. The transcriptional activity of both templates was inhibited by increasing amounts of histone H1, although inhibition with the methylated template occurs at a lower H1:DNA ratio. The H1c variant shows the greatest preferential inhibition of the methylated template. We demonstrated that histone H1 complexed to DNA is one of the factors that inhibits transcription by preventing the formation of initiation complexes, particularly on methylated template, rather than the formation of disordered H1.DNA aggregates.

Molecular characterization and expression of a tobacco histone H1 cDNA

We have isolated a 1104 bp tobacco cDNA clone (H1c12) which includes an 846 bp open reading frame. This encodes a polypeptide of 282 amino acid residues and represents the largest plant H1 histone identified so far. The structure of the deduced protein shows the classical tripartite organization of the H1-type linker histones. The expression of the tobacco H1 histone gene(s) corresponding to the H1c12 cDNA clone was examined during different developmental stages. We found that, at the level of steady-state mRNA, expression of gene(s) encoding this H1 histone was rapidly induced in germinating seeds. The H1 gene was expressed in all tissues examined. However, its expression was higher in tissues known to contain meristematic cells. Furthermore, in the leaves of mature plants accumulation of the H1 mRNA exhibits a very characteristic oscillation. This latter finding indicates that, at least in fully developed plants, the expression of this type of H1 histone gene(s) is modulated by a diurnal cycle.

Affinity enrichment and functional characterization of TRAX1, a novel transcription activator and X1-sequence-binding protein of HLA-DRA

The promoters of all class II major histocompatibility (MHC) genes contain a positive regulatory motif, the X element. The DNA-binding proteins specific for this element are presumed to play a critical role in gene expression, although there is a paucity of functional studies supporting this role. In this study, the X-box-binding proteins of HLA-DRA were affinity purified from HeLa nuclear extracts. Fractions 46 to 48 contained an X-box-binding activity and were determined by electrophoretic mobility shift assays to be specific for the X1 element. This X1 sequence-binding-protein, transcriptional activator X1 (TRAX1), was shown to be a specific transcriptional activator of the HLA-DRA promoter in an in vitro transcription assay. By UV cross-linking analysis, the approximate molecular mass of TRAX1 including the bound DNA was determined to be 40 kDa. When the TRAX1 complex was incubated with antibodies against a known recombinant X-box-binding protein, RFX1, and tested in electrophoretic mobility shift assays, TRAX1 was neither shifted nor blocked by the antibody. Further analysis with methylation interference showed that TRAX1 bound to the 5' end of the X1 sequence at -109 and -108 and created hypersensitive sites at -114, -113, and -97. This methylation interference pattern is distinct from those of the known X1-binding proteins RFX1, RFX, NF-Xc, and NF-X. Taken together, our results indicate that TRAX1 is a novel X1-sequence-binding protein and transcription activator of HLA-DRA.

Mouse mammary tumor virus chromatin in human breast cancer cells is constitutively hypersensitive and exhibits steroid hormone-independent loading of transcription factors in vivo

We have stably introduced a reporter gene under the control of the mouse mammary tumor virus (MMTV) long terminal repeat (LTR) into human T47D breast cancer cells to study the action of the progesterone receptor (PR) on transcription from a chromatin template. Unexpectedly, the chromatin organization of the MMTV LTR in these human breast cancer cells differed markedly from what we have observed previously. The region adjacent to the transcription start site (-221 to -75) was found to be constitutively hypersensitive to restriction enzyme cleavage in the absence of hormone. This region is normally encompassed within the second nucleosome of a phased array of six nucleosomes that is assembled when the MMTV LTR is stably maintained in mouse cells. Characteristically, in these rodent cells, the identical DNA sequences show increased restriction enzyme cleavage only in the presence of glucocorticoid. The increased access of restriction enzymes observed in the human PR+ cells was not observed in adjacent nucleosomes and was unaffected by treatment with the progesterone antagonist RU486. In addition, exonuclease III-dependent stops corresponding to the binding sites for nuclear factor 1 and the PR were observed before and after hormone treatment. These results indicate that MMTV chromatin replicated in these cells is organized into a constitutively open architecture and that this open chromatin state is accompanied by hormone-independent loading of a transcription factor complex that is normally excluded from uninduced chromatin.

Chromatin structure determines the sites of chromosome breakages in Plasmodium falciparum

Spontaneous chromosome breakages are frequently observed in the human malaria parasite Plasmodium falciparum and are responsible for the generation of novel phenotypes, which may contribute to the pathogenicity and virulence of this protozoan parasite. The identification of a hot spot of chromosome breakage within the coding region of the KAHRP gene revealed that these events do not occur randomly but follow a regular pattern with a periodicity of 155 bp. This phasing corresponds to the average repeat unit of P. falciparum nucleosomes. Furthermore, breakage events preferentially occur within the linker regions of nucleosomes, as demonstrated by mapping endonuclease hypersensitive sites of chromatin. These data suggest that, in P. falciparum, the chromatin structure is involved in the molecular process of chromosome breakage, a mechanism that may be common in other eukaryotes.

The establishment of active promoters in chromatin

The organization of eukaryotic genomes as chromatin provides the framework within which regulated transcription occurs in the nucleus. The association of DNA with chromatin proteins required to package the genome into the nucleus is, in general, inhibitory to transcription, and therefore provides opportunities for regulated transcriptional activation. Granting access to the cis-acting elements in DNA, a prerequisite for any further action of the trans-acting factors involved, requires the establishment of local heterogeneity of chromatin and, in some cases, extensive remodeling of nucleosomal structures. Challenging problems relate to the establishment of this heterogeneity at the level of the single nucleosome and to the mechanisms that operate when nucleosomal arrays are reorganized. Recent developments indicate that chromatin reconstitution in cell-free systems allows the biochemical analysis of the interplay between transcription factors and chromatin components that brings about regulated transcription.

Transcriptional activation. Switched-on chromatin

A large 'SWI/SNF' general activator complex serves as a molecular machine to help a wide range of transcription factors overcome the specific repressive effects of chromatin.

Nucleosome positioning and modification: chromatin structures that potentiate transcription

The role of the nucleosome in the folding of DNA has often been thought of as purely a packaging one. However, the precise folding of regulatory sequences of genes around the histones within positioned nucleosomes is also important in controlling both the access of transcription factors to chromatin and the transcription process itself. This review highlights these functions by using specific examples of an active and regulatory role for positioned nucleosomes.

Transcription: in tune with the histones

The regulation of transcription in eukaryotes relies upon the histone proteins in several essential ways. The incorporation of the binding sites for the basal transcriptional machinery into nucleosomes serves to repress transcription. Specific regulatory molecules other than the basal transcriptional machinery exist that can associate with nucleosomal DNA and initiate a chain of events that disrupt repressive histone-DNA complexes. The main players in this story have been defined physically and genetically and include positioned nucleosomes, interactions of the histone tetramer (H3-H4)2 with DNA, the N-terminal tails of histones H3 and H4, and a large general activator complex. How they fit together biochemically is yet to be defined. The genetic data demonstrate that the disruption of histone-DNA complexes plays a major role in the induction of transcription from many genes. However, not all genes are repressed by nucleosome assembly: certain promoters make use of the staged assembly of chromatin in vivo and a rapid and tight association of transacting factors with promoter elements to remain constitutively active. Moreover, nucleosome assembly is not necessarily repressive, since the folding of DNA by the histones can facilitate the activation of genes by bringing widely separated regulatory elements into juxtaposition. Thus, histones provide the necessary infrastructure for the correct and efficient operation of the transcriptional machinery; however, their exact contributions to the transcriptional regulation of an individual gene may depend on the spatial distribution of regulatory elements, the transcription factors involved, and the three-dimensional folding of DNA that they direct.

Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures

The DNA in a eukaryotic nucleus is packaged into a nucleosome array, punctuated by variations in the regular pattern. The local chromatin structure of inducible genes appears to fall into two categories: preset and remodeling. Preset genes are those in which the binding sites for trans-acting factors are accessible (i.e. in a non-nucleosomal, DNase I hypersensitive configuration) prior to activation. In response to the activation signal, positive factors bind to cis-acting regulatory elements and trigger transcription with no major alterations in the chromatin structure of the promoter region. In contrast, remodeling genes are those in which some of the required cis-acting regulatory elements are packaged into nucleosomes. The nucleosomes must be perturbed in response to an activation signal in order for the trans-acting factors to gain access to cis-acting elements; a chromatin remodeling process which forms DNase I hypersensitive sites must occur. In both cases, precise positioning of nucleosomes along the promoter region of a gene appears to be critical for appropriate regulation of expression.

Dual promoter activation by the human beta-globin locus control region

The human beta-globin locus control region (LCR) is necessary for high-level and position-independent expression of globin genes in erythroid cells. A variety of mechanisms have been proposed for the cis-activation of individual members of the beta-globin gene family by the LCR located 10-50 kilobases upstream. It is not known, however, whether a given LCR can activate all developmentally appropriate globin family members on its chromosome or whether, within a given chromosome, the LCR must be committed to activating only a single gene. We have devised an experiment to distinguish between these possibilities. This experiment takes advantage of the fact that if two genes in a cluster are transcriptionally active and their promoters, therefore, are in a conformation hypersensitive to nucleases, restriction enzymes that cleave the promoters will excise the intervening chromatin fragment. The Apa I sites on human fetal G gamma- and A gamma-globin gene promoters are accessible to cleavage in nuclei from the human erythroleukemia cell line K562, which expresses these genes, but not in HeLa cells. We find that Apa I digestion leads to excision in high yield of the fragment spanning these promoters, showing that a LCR element is capable of sharing its activating function among members of a gene cluster on a single chromosome.

A histone octamer can step around a transcribing polymerase without leaving the template

The mechanism by which nucleosome cores are displaced and re-formed during transcription in vitro has been investigated. A nucleosome core was assembled on a short linear DNA template (227 bp) containing an SP6 RNA polymerase promoter and a nucleosome-positioning sequence. Transcription induced the translocation of the nucleosome core over 75 or 80 bp to two positions at the other end of the template, blocking the promoter. At low rNTP concentrations, transfer occurred only on the same template molecule, even in the presence of large excesses of competitor DNA. On a longer template (262 bp), nucleosome core position after transcription depended on its position before transcription. The data suggest that the octamer transfers without dissociation from DNA and provide strong evidence for a translocation mechanism in which DNA ahead of the polymerase uncoils from the octamer as the DNA behind coils around it. In this way, the octamer steps around the transcribing polymerase.

Chromatin structure and the expression of globin-encoding genes

The developmental regulation of globin gene expression in the chicken has been studied. All of the genes are regulated by a small number of general erythroid factors. In addition, expression of individual members of the family must be controlled in a lineage (stage)-specific manner. In some cases, the relevant factors may be stage specific, but in others they are not confined to one stage, but exert their control through developmentally regulated changes in their abundance within the nucleus. Chromatin structural elements, such as locus control regions and insulators, are also involved in control of eukaryotic gene expression. Because so much is understood about regulation of individual genes, the globin family has proven valuable in investigating control of transcription at the level of chromatin structure.

Parental nucleosomes segregated to newly replicated chromatin are underacetylated relative to those assembled de novo

Antibodies specific for acetylated histone H4 were used to examine the acetylation state of parental histones that segregate to newly replicated DNA. To generate newly replicated chromatin containing only segregated parental nucleosomes, isolated nuclei were labeled with [3H]TTP in vitro; alternatively, whole cells were labeled with [3H]thymidine in the presence of cycloheximide. Soluble chromatin was prepared by micrococcal nuclease digestion, and subjected to immunoprecipitation with "penta" antibodies (Lin et al., 1989). In sharp contrast to nucleosomes containing newly synthesized, diacetylated H4 (Perry et al., 1993), chromatin replicated in vitro was only marginally susceptible to immunoprecipitation. Control experiments established that bona fide acetylated chromatin was selectively immunoprecipitated by the same techniques and that segregated nucleosomes were not disassembled during treatment with "penta" antibodies. When replication was coupled to an in vitro histone acetylation system, the enrichment for segregated nucleosomes in the immunopellet increased approximately 3-fold, demonstrating that changes in the acetylation state of segregated histones can be detected immunologically and that parental histones on new DNA are accessible to acetyltransferases during, or immediately after, DNA replication. In vivo pulse-chase experiments, performed in the presence of cycloheximide, confirmed these results. Uptake experiments further established that concurrent histone acetylation did not alter the rate of DNA synthesis in vitro. Our results provide evidence that replication-competent chromatin is not obligatorily acetylated, and indicate that the acetylation status of segregated histones may be maintained during chromatin replication. The possible significance of this, with respect to the regulation of chromatin higher order structures during DNA replication, and the propagation of transcriptionally active vs inactive chromatin structures, is discussed.

Two motion systems with common and separate pathways for color and luminance

We present psychological experiments that reveal two motion systems, a specific and an unspecific one. The specific system prevails at medium to high temporal frequencies. It comprises at least two separate motion pathways that are selective for color and for luminance and that do not interact until after the motion signal is extracted separately in each. By contrast, the unspecific system prevails at low temporal frequencies and it combines color and luminance signals at an earlier stage, before motion extraction. The successful implementation of an efficient and accurate technique for assessing equiluminance corroborates further the main findings. These results offer a general framework for understanding the nature of interactions between color and luminance signals in motion perception and suggest that previously proposed dichotomies in motion processing may be encompassed by the specific/unspecific dichotomy proposed here.

Newly expressed progesterone receptor cannot activate stable, replicated mouse mammary tumor virus templates but acquires transactivation potential upon continuous expression

During development and differentiation, the expression of transcription factors is regulated in a temporal fashion. Newly expressed transcription factors must interact productively with target genes organized in chromatin. Although the mechanisms governing factor binding to chromatin templates are not well understood, it is now clear that template access can be dramatically influenced by nucleoprotein structure. We have examined the ability of a well characterized transactivator, the progesterone receptor (PR), to activate the mouse mammary tumor virus (MMTV) promoter organized either in stable, replicating templates that have a highly ordered nucleosome structure or as transiently transfected DNA, which adopts a less-defined structure. If the PR is transiently expressed in cells harboring both replicated and transient MMTV receptor constructs, it cannot significantly activate the stable replicated MMTV template. In contrast, when PR cDNA is stably inserted into the same cells and constitutively expressed, it gains the ability to activate both chromosomal and transiently introduced templates. These results demonstrate that newly expressed PR is not competent to activate the MMTV template in its native nucleoprotein conformation but acquires this ability upon prolonged expression in replicating cells.