Differential dissociation of histone tails from core chromatin

The macromolecular complexes of histones affect protein arginine methyltransferase activities

Histone arginine methylation is a key post-translational modification that mediates epigenetic events that activate or repress gene transcription. Protein arginine methyltransferases (PRMTs) are the driving force for the process of arginine methylation, and the core histone proteins have been shown to be substrates for most PRMT family members. However, previous reports of the enzymatic activities of PRMTs on histones in the context of nucleosomes seem contradictory. Moreover, what governs nucleosomal substrate recognition of different PRMT members is not understood. We sought to address this key biological question by examining how different macromolecular contexts where the core histones reside may regulate arginine methylation catalyzed by individual PRMT members (i.e., PRMT1, PRMT3, PRMT4, PRMT5, PRMT6, PRMT7, and PRMT8). Our results demonstrated that the substrate context exhibits a huge impact on the histone arginine methylation activity of PRMTs. Although all the tested PRMTs methylate multiple free histones individually, they show a preference for one particular histone substrate in the context of the histone octamer. We found that PRMT1, PRMT3, PRMT5, PRMT6, PRMT7, and PRMT8 preferentially methylate histone H4, whereas PRMT4/coactivator-associated arginine methyltransferase 1 prefers histone H3. Importantly, neither reconstituted nor cell-extracted mononucleosomes could be methylated by any PRMTs tested. Structural analysis suggested that the electrostatic interaction may play a mechanistic role in priming the substrates for methylation by PRMT enzymes. Taken together, this work expands our knowledge on the molecular mechanisms of PRMT substrate recognition and has important implications for understanding cellular dynamics and kinetics of histone arginine methylation in regulating gene transcription and other chromatin-templated processes.

Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA

The interaction of positively charged N-terminal histone tails with nucleosomal DNA plays an important role in chromatin assembly and regulation, modulating their susceptibility to post-translational modifications and recognition by chromatin-binding proteins. Here, we report residue-specific ¹⁵ N NMR relaxation rates for histone H4 tails in reconstituted nucleosomes. These data indicate that H4 tails are strongly dynamically disordered, albeit with reduced conformational flexibility compared to a free peptide with the same sequence. Remarkably, the NMR observables were successfully reproduced in a 2-μs MD trajectory of the nucleosome. This is an important step toward resolving an apparent inconsistency where prior simulations were generally at odds with experimental evidence on conformational dynamics of histone tails. Our findings indicate that histone H4 tails engage in a fuzzy interaction with nucleosomal DNA, underpinned by a variable pattern of short-lived salt bridges and hydrogen bonds, which persists at low ionic strength (0-100 mM NaCl).

Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR

NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.

On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function

Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is 'translated' to the particular 'activating' or 'repressing' chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content - such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products) of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a 'polymer' of individual 'canonical' nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.

A brief review of nucleosome structure

The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.

Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure

Eukaryotic chromatin is a hierarchical collection of nucleoprotein structures that package DNA to form chromosomes. The initial levels of packaging include folding of long strings of nucleosomes into secondary structures and array-array association into higher-order tertiary chromatin structures. The core histone tail domains are required for the assembly of higher-order structures and mediate short- and long-range intra- and inter-nucleosome interactions with both DNA and protein targets to direct their assembly. However, important details of these interactions remain unclear and are a subject of much interest and recent investigations. Here, we review work defining the interactions of the histone N-terminal tails with DNA and protein targets relevant to chromatin higher-order structures, with a specific emphasis on the contributions of H3 and H4 tails to oligonucleosome folding and stabilization. We evaluate both classic and recent experiments determining tail structures, effect of tail cleavage/loss, and posttranslational modifications of the tails on nucleosomes and nucleosome arrays, as well as inter-nucleosomal and inter-array interactions of the H3 and H4 N-terminal tails.

Secondary structures of the core histone N-terminal tails: their role in regulating chromatin structure

The core histone N-terminal tails dissociate from their binding positions in nucleosomes at moderate salt concentrations, and appear unstructured in the crystal. This suggested that the tails contributed minimally to chromatin structure. However, in vitro studies have shown that the tails were involved in a range of intra- and inter-nucleosomal as well as inter-fibre contacts. The H4 tail, which is essential for chromatin compaction, was shown to contact an adjacent nucleosome in the crystal. Acetylation of H4K16 was shown to abolish the ability of a nucleosome array to fold into a 30 nm fibre. The application of secondary structure prediction software has suggested the presence of extended structured regions in the histone tails. Molecular Dynamics studies have further shown that sections of the H3 and H4 tails assumed α-helical and β-strand content that was enhanced by the presence of DNA, and that post-translational modifications of the tails had a major impact on these structures. Circular dichroism and NMR showed that the H3 and H4 tails exhibited significant α-helical content, that was increased by acetylation of the tail. There is thus strong evidence, both from biophysical and from computational approaches, that the core histones tails, particularly that of H3 and H4, are structured, and that these structures are influenced by post-translational modifications. This chapter reviews studies on the position, binding sites and secondary structures of the core histone tails, and discusses the possible role of the histone tail structures in the regulation of chromatin organization, and its impact on human disease.

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear ε-oligo(L-lysines), (denoted εKn, n = 3–10, 31; n is the number of lysines with the ligand charge Z = n+1) and branched α-substituted homologues of εK10: εYK10, εLK10 (Z = +11); εRK10, εYRK10 and εLYRK10 (Z = +21). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, CKCl). The dependence of EC50 (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC50 with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC50 dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand–DNA complex is derived. For the ε-oligolysines εK6–εK10, the experimental dependencies of EC50 on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.

Cation-induced polyelectrolyte-polyelectrolyte attraction in solutions of DNA and nucleosome core particles

The paper reviews our current studies on the experimentally induced cation compaction and aggregation in solutions of DNA and nucleosome core particles and the theoretical modelling of these processes using coarse-grained continuum models with explicit mobile ions and with all-atom molecular dynamics (MD) simulations. Recent experimental results on DNA condensation by cationic oligopeptides and the effects of added salt are presented. The results of MD simulations modelling DNA-DNA attraction due to the presence of multivalent ions including the polyamine spermidine and fragments of histone tails, which exhibit bridging between adjacent DNA molecules, are discussed. Experimental data on NCP aggregation, using recombinantly prepared systems are summarized. Literature data and our results of studying of the NCP solutions are compared with predictions of coarse-grained MD simulations, including the important ion correlation as well as bridging mechanisms. The importance of the results to chromatin folding and aggregation is discussed.

A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear epsilon-oligo(l-lysines), (denoted epsilonKn, n = 3-10, 31; n is the number of lysines equal to the ligand charge) and branched alpha-substituted homologues of epsilonK10: epsilonYK10, epsilonLK10 (Z = +10); epsilonRK10, epsilonYRK10 and epsilonLYRK10 (Z = +20). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, C(KCl)). The dependence of EC(50) (ligand concentration at the midpoint of DNA condensation) on C(KCl) shows the existence of a salt-independent regime at low C(KCl) and a salt-dependent regime with a steep rise of EC(50) with increase of C(KCl). Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher C(KCl). A novel and simple relationship describing the EC(50) dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand-DNA complex is derived. For the epsilon-oligolysines epsilonK3-epsilonK10, the experimental dependencies of EC(50) on C(KCl) and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.

Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles

Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg(2+)), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg(2+). Simulations for systems with a gradual substitution of K(+) for Mg(2+), to mimic the Mg(2+) titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg(2+), compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the histone tails from the globular NCP is not in itself a major factor in NCP-NCP aggregation. The approximation of coarse-graining, with respect to the description of the NCP as a sphere with uniform charge distribution, was tested in control simulations. A more detailed description of the NCP did not change the main features of the results. Overall, the results of this work are in agreement with experimental data reported for NCP solutions and for chromatin arrays.

Genetic and epigenetic alterations in breast cancer: what are the perspectives for clinical practice?

The worldwide incidence of breast cancer affects 1.2 million women each year. In contrast to the high occurrence of this malady, a decline in mortality is reported among industrialized countries. In this respect, both awareness campaigns and substantial progress achieved in therapy and diagnosis allowed for the enhancement of the survival rate in patients with breast cancer. Undoubtedly, oncology research programs played a relevant role in the improvement of therapeutics and diagnostics for breast cancer. Major strides were reported, especially over the last decade and a half, in better understanding molecular and cellular biology events involved in breast cancer pathogenesis and progression of the disease. However, therapeutic approaches for the treatment of patients with breast cancer need further improvement. Therapeutic interventions can chronically compromise both the state of health and quality of life of breast cancer survivors. In addition, current therapeutic approaches have not significantly improved the survival rate in patients with metastatic disease. On these grounds, it is necessary to develop more efficient therapeutics and diagnostic tools, which can improve the health and quality of life of breast cancer survivors and increase the survival rate in patients with metastatic disease. In this respect, the field of cancer research has placed a particular emphasis on the elucidation of genetic and epigenetic alterations that may lead to the pathogenesis of breast cancer and contribute to its progression.

Site-specific binding affinities within the H2B tail domain indicate specific effects of lysine acetylation

Acetylation of specific lysines within the core histone tail domains plays a critical role in regulating chromatin-based activities. However, the structures and interactions of the tail domains and the molecular mechanisms by which acetylation directly alters chromatin structures are not well understood. To address these issues we developed a chemical method to quantitatively determine binding affinities of specific regions within the individual tail domains in model chromatin complexes. Examinations of specific sites within the H2B tail domain indicate that this tail contains distinct structural elements and binds within nucleosomes with affinities that would reduce the activity of tail-binding proteins 10-50-fold from that deduced from peptide binding studies. Moreover, we find that mutations mimicking lysine acetylation do not cause a global weakening of tail-DNA interactions but rather the results suggest that acetylation leads to a much more subtle and specific alteration in tail interactions than has been assumed. In addition, we provide evidence that acetylation at specific sites in the tail is not additive with several events resulting in similar, localized changes in tail binding.

H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

All-atom molecular dynamics (MD) simulations were performed during 30-45 ns for a system of three identical DNA 22-mers, 14 short fragments of the charged H4 histone tail peptide fragment (amino acids 5-12, KGGKGLGK) with K(+) counterions, and explicit water. The simulation setup mimics the crowded conditions of DNA in eukaryotic chromatin. To assess the influence of tail fragments on DNA structure and dynamics, a "control" 20 ns MD simulation was carried for a system with the same DNA and water content but in the absence of oligopeptides. Results of DNA interaction with the histone tail fragments, K(+), and water is presented. DNA structure and dynamics and its interplay with the histone tail fragments binding are described. The charged side chains of the lysines play a major role in mediating DNA-DNA attraction by forming bridges and coordinating to phosphate groups and electronegative sites in the minor groove. Binding of all species to DNA is dynamic. Some of the tail fragments while being flexible and mobile in each of its functional groups remain associated near certain locations of the DNA oligomer. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction, and dynamics.

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical approach, outlines the major findings, and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder.

Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histones

Chromatin is composed of genomic DNA and histones, forming a hierarchical architecture in the nucleus. The chromatin hierarchy is common among eukaryotes despite different intrinsic properties of the genome. To investigate an effect of the differences in genome organization, chromatin unfolding processes were comparatively analyzed using Schizosaccaromyces pombe, Saccharomyces cerevisiae, and chicken erythrocyte. NaCl titration showed dynamic changes of the chromatin. 400-1000 mM NaCl facilitated beads with approximately 115 nm in diameter in S. pombe chromatin. A similar transition was also observed in S. cerevisiae chromatin. This process did not involve core histone dissociation from the chromatin, and the persistence length after the transition was approximately 26 nm for S. pombe and approximately 28 nm for S. cerevisiae, indicating a salt-induced unfolding to "beads-on-a-string" fibers. Reduced salt concentration recovered the original structure, suggesting that electrostatic interaction would regulate this discrete folding-unfolding process. On the other hand, the linker histone was extracted from chicken chromatin at 400 mM NaCl, and AFM observed the "beads-on-a-string" fibers around a nucleus. Unlike yeast chromatin, therefore, this unfolding was irreversible because of linker histone dissociation. These results indicate that the chromatin unfolding and refolding depend on the presence and absence of the linker histone, and the length of the linker DNA.

Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations

Electrostatic interactions between DNA and DNA-packaging proteins, the histones, contribute substantially to stability of eukaryotic chromatin on all levels of its organization and are particularly important in formation of its elementary structural unit, the nucleosome. The release of DNA from the histones is an unavoidable stage in reading the DNA code. In the present review, we discuss the disassembly/assembly process of the nucleosome from a thermodynamic standpoint by considering it as a competition between an excess of polyanions (DNA and acidic/phosphorylated domains of the nuclear proteins) for binding to a limited pool of polycations (the histones). Results obtained in model systems are used to discuss conditions for the electrostatic component of DNA-protein interactions contributing to chromatin statics and dynamics. We propose a simple set of "electrostatic conditions" for the disassembly/assembly of nucleosome/chromatin and apply these to put forward a number of new interpretations for the observations reported in literature on chromatin. The approach sheds light on the functions of acidic domains in the nuclear proteins (nucleoplasmin and other histone chaperones, HMG proteins, the activation domains in transcriptional activators). It results in a putative explanation for the molecular mechanisms behind epigenetic regulation through histone acetylation, phosphorylation, and other alterations ("the language of covalent histone modification"). We also propose a new explanation for the role of phosphorylation of C-terminal domain of RNA polymerase II for regulation of the DNA transcription. Several other examples from literature on chromatin are discussed to support applicability of electrostatic rules for description of chromatin structure and dynamics.

Physical methods used to study core histone tail structures and interactions in solutionThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process

The core histone tail domains are key regulatory elements in chromatin. The tails are essential for folding oligonucleosomal arrays into both secondary and tertiary structures, and post-translational modifications within these domains can directly alter DNA accessibility. Unfortunately, there is little understanding of the structures and interactions of the core histone tail domains or how post-translational modifications within the tails may alter these interactions. Here we review NMR, thermal denaturation, cross-linking, and other selected solution methods used to define the general structures and binding behavior of the tail domains in various chromatin environments. All of these methods indicate that the tail domains bind primarily electrostatically to sites within chromatin. The data also indicate that the tails adopt specific structures when bound to DNA and that tail structures and interactions are plastic, depending on the specific chromatin environment. In addition, post-translational modifications, such as acetylation, can directly alter histone tail structures and interactions.

SCN- binding to the charged lysines of histones end domains mimics acetylation and shows the major histone-DNA interactions involved in eu and heterochromatin stabilization

SCN- binds to the charged amino group of lysines, inducing local changes in the electrostatic free energy of histones. We exploited this property to selectively perturb the histone-DNA interactions involved in the stabilization of eu and heterochromatin. Differential scanning calorimetry (DSC) was used as leading technique in combination with trypsin digestion that selectively cleaves the histone end domains. Euchromatin undergoes progressive destabilization with increasing KSCN concentration from 0 to 0.3 M. Trypsin digestion in the presence of 0.2 M KSCN show that the stability of the linker decreases as a consequence of the competitive binding of SCN- to the amino groups located in the C and N-terminal domain of H1 and H3, respectively; likewise, the release of the N-terminal domain of H4 induces an appreciable depression in both the temperature and enthalpy of melting of core particle DNA. Unfolding of heterochromatin requires, in addition to further cleavage of H4, extensive digestion of H2A and H2B, strongly suggesting that these histones stabilize the higher order structure by forming a protein network which extends throughout the heterochromatin domain.

Biochemical screening of stable dinucleosomes using DNA fragments from a dinucleosome DNA library

The dinucleosome is an informative unit for analysis of the higher-order chromatin structure. DNA fragments forming stable dinucleosomes were screened from a dinucleosome DNA library after the reconstitution of nucleosomes in vitro and digestion with micrococcal nuclease. Reconstituted dinucleosomes showed a diversity of sensitivity to micrococcal nuclease, suggesting that the biochemical stability of a dinucleosome depends, in part, on the DNA fragments. The DNA fragments after the screening were classified into three groups represented by clones bf10, af14 and af32 according to the sensitivity to micrococcal nuclease. Mapping of the nucleosome boundaries by Southern blotting of the DNA after restriction digestion and by primer extension analysis showed that each nucleosome position of clone af32 was fixed. Analysis of reconstituted dinucleosomes using mutant DNA fragments of clone af32 revealed a unique property characteristic of a key nucleosome, given that the replacement of a DNA fragment corresponding to the right nucleosome position resulted in marked sensitivity to micrococcal nuclease, whereas the replacement of the other nucleosome fragment had almost no effect on sensitivity as compared to the original af32 construct. The mutant construct in which the right nucleosome was removed showed multiple nucleosome phases, suggesting that the right nucleosome stabilized first each mononucleosome and then the dinucleosome. An oligonucleotide bending assay revealed that the DNA fragment in the right nucleosome included curved DNA, suggesting that the positioning activity of the nucleosome was attributed to its DNA structure. These results suggest that information for forming stable dinucleosome is embedded in the genomic DNA and that a further characterization of the key nucleosome is useful for understanding the building up of the chromatin structure.

Dominant role of smooth muscle L-type calcium channel Cav1.2 for blood pressure regulation

Blood pressure is regulated by a number of key molecules involving G-protein-coupled receptors, ion channels and monomeric small G-proteins. The relative contribution of these different signaling pathways to blood pressure regulation remains to be determined. Tamoxifen-induced, smooth muscle-specific inactivation of the L-type Cav1.2 Ca2+ channel gene in mice (SMAKO) reduced mean arterial blood pressure (MAP) in awake, freely moving animals from 120 +/- 4.5 to 87 +/- 8 mmHg. Phenylephrine (PE)- and angiotensin 2 (AT2)-induced MAP increases were blunted in SMAKO mice, whereas the Rho-kinase inhibitor Y-27632 reduced MAP to the same extent in control and SMAKO mice. Depolarization-induced contraction was abolished in tibialis arteries of SMAKO mice, and development of myogenic tone in response to intravascular pressure (Bayliss effect) was absent. Hind limb perfusion experiments suggested that 50% of the PE-induced resistance is due to calcium influx through the Cav1.2 channel. These results show that Cav1.2 calcium channels are key players in the hormonal regulation of blood pressure and development of myogenic tone.

Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system

The core histone tail domains are key regulators of eukaryotic chromatin structure and function and alterations in the tail-directed folding of chromatin fibers and higher order structures are the probable outcome of much of the post-translational modifications occurring in these domains. The functions of the tail domains are likely to involve complex intra- and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. Here we introduce a method for examining inter-nucleosome interactions of the tail domains in a model dinucleosome and determine the propensity of each of the four N-terminal tail domains to mediate such interactions in this system. Using a strong nucleosome "positioning" sequence, we reconstituted a nucleosome containing a single histone site specifically modified with a photoinducible cross-linker within the histone tail domain, and a second nucleosome containing a radiolabeled DNA template. These two nucleosomes were then ligated together and cross-linking induced by brief UV irradiation under various solution conditions. After cross-linking, the two templates were again separated so that cross-linking representing inter-nucleosomal histone-DNA interactions could be unambiguously distinguished from intra-nucleosomal cross-links. Our results show that the N-terminal tails of H2A and H2B, but not of H3 and H4, make internucleosomal histone-DNA interactions within the dinucleosome. The relative extent of intra- to inter-nucleosome interactions was not strongly dependent on ionic strength. Additionally, we find that binding of a linker histone to the dinucleosome increased the association of the H3 and H4 tails with the linker DNA region.

Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions

Chromatin fibers are dynamic macromolecular assemblages that are intimately involved in nuclear function. This review focuses on recent advances centered on the molecular mechanisms and determinants of chromatin fiber dynamics in solution. Major points of emphasis are the functions of the core histone tail domains, linker histones, and a new class of proteins that assemble supramolecular chromatin structures. The discussion of important structural issues is set against a background of possible functional significance.

Salt-induced conformation and interaction changes of nucleosome core particles

Small angle x-ray scattering was used to follow changes in the conformation and interactions of nucleosome core particles (NCP) as a function of the monovalent salt concentration C(s). The maximal extension (D(max)) of the NCP (145 +/- 3-bp DNA) increases from 137 +/- 5 A to 165 +/- 5 A when C(s) rises from 10 to 50 mM and remains constant with further increases of C(s) up to 200 mM. In view of the very weak increase of the R(g) value in the same C(s) range, we attribute this D(max) variation to tail extension, a proposal confirmed by simulations of the entire I(q) curves, considering an ideal solution of particles with tails either condensed or extended. This tail extension is observed at higher salt values when particles contain longer DNA fragments (165 +/- 10 bp). The maximal extension of the tails always coincides with the screening of repulsive interactions between particles. The second virial coefficient becomes smaller than the hard sphere virial coefficient and eventually becomes negative (net attractive interactions) for NCP(145). Addition of salt simultaneously screens Coulombic repulsive interactions between NCP and Coulombic attractive interactions between tails and DNA inside the NCP. We discuss how the coupling of these two phenomena may be of biological relevance.

Preferential interaction of the core histone tail domains with linker DNA

Within chromatin, the core histone tail domains play critical roles in regulating the structure and accessibility of nucleosomal DNA within the chromatin fiber. Thus, many nuclear processes are facilitated by concomitant posttranslational modification of these domains. However, elucidation of the mechanisms by which the tails mediate such processes awaits definition of tail interactions within chromatin. In this study we have investigated the primary DNA target of the majority of the tails in mononucleosomes. The results clearly show that the tails bind preferentially to "linker" DNA, outside of the DNA encompassed by the nucleosome core. These results have important implications for models of tail function within the chromatin fiber and for in vitro structural and functional studies using nucleosome core particles.

Acetylation increases the alpha-helical content of the histone tails of the nucleosome

The nature of the structural changes induced by histone acetylation at the different levels of chromatin organization has been very elusive. At the histone level, it has been proposed on several occasions that acetylation may induce an alpha-helical conformation of their acetylated N-terminal domains (tails). In an attempt to provide experimental support for this hypothesis, we have purified and characterized the tail of histone H4 in its native and mono-, di-, tri-, and tetra- acetylated form. The circular dichroism analysis of these peptides shows conclusively that acetylation does increase their alpha-helical content. Furthermore, the same spectroscopic analysis shows that this is also true for both the acetylated nucleosome core particle and the whole histone octamer in solution. In contrast to the native tails in which the alpha-helical organization appears to be dependent upon interaction of these histone regions with DNA, the acetylated tails show an increase in alpha-helical content that does not depend on such an interaction.

Spermidine-induced aggregation of nucleosome core particles: evidence for multiple liquid crystalline phases

We investigate the effect of the addition of a trivalent cation, spermidine, to dilute solutions of nucleosome core particles (NCP). In the presence of spermidine, part of the NCP segregates from the initial homogeneous solution, forming dense aggregates. We follow this precipitation process over a wide range of spermidine and NaCl concentrations and determine the conditions of aggregation of the particles. The structure of the dense phases is analyzed by means of polarizing light microscopy and cryo-electron microscopy. We report the existence of multiple supramolecular organizations. According to the relative concentrations of spermidine, monovalent salt and NCP, the particles may aggregate into amorphous phases, stack into randomly oriented columns, or form liquid crystalline phases. Two discotic liquid crystalline phases are identified and analyzed: a columnar nematic corresponding to columns of NCP simply aligned in parallel, and a columnar hexagonal phase in which the columns order into a transversal 2D hexagonal array. We discuss the nature and origin of the interactions possibly involved in the formation and maintenance of these different types of order.

Chromatin disruption and modification

Chromatin disruption and modification are associated with transcriptional regulation by diverse coactivators and corepressors. Here we discuss the possible structural basis and functional consequences of the observed alterations in chromatin associated with transcriptional activation and repression. Recent advances in defining the roles of individual histones and their domains in the assembly and maintenance of regulatory architectures provide a framework for understanding how chromatin remodelling machines, histone acetyltransferases and deacetylases function.

Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding

In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

Transcriptional inhibitory role of the tail domains of histone (H3 x H4)2 tetramers

Histone-DNA templates for bacteriophage T7 RNA polymerase were assembled from a plasmid containing a promoter and a terminator for this polymerase, (H3 x H4)2 tetramers deprived of their tail domains, and H2A x H2B dimers. Histone (H3 x H4)2 tetramers lacking their terminal domains were obtained from trypsin-digested nucleosomal cores. The oligonucleosomal templates containing (H3 x H4)2 tetramers lacking their tail domains, like the control templates with intact core histone octamers, protect approximately 146 base pairs of DNA against micrococcal nuclease digestion. The transcriptional inhibition caused by the association of DNA with core histone octamers is significantly reduced upon elimination of the tail domains of the (H3 x H4)2 tetramers. Apparently, the terminal domains of (H3 x H4)2 must be present to block transcription efficiently. These results show the important inhibitory role played by the tail domains of the histone (H3 x H4)2 tetramers, suggesting the involvement of these regions in transcriptional regulation.

Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin

A number of activators are known to increase transcription by RNA polymerase (pol) II through protein acetylation. While the physiological substrates for those acetylases are poorly defined, possible targets include general transcription factors, activator proteins and histones. Using a cell-free system to reconstitute chromatin with increased histone acetylation levels, we directly tested for a causal role of histone acetylation in transcription by RNA pol II. Chromatin, containing either control or acetylated histones, was reconstituted to comparable nucleosome densities and characterized by electron microscopy after psoralen cross-linking as well as by in vitro transcription. While H1-containing control chromatin severely repressed transcription of our model hsp26 gene, highly acetylated chromatin was significantly less repressive. Acetylation of histones, and particularly of histone H4, affected transcription at the level of initiation. Monitoring the ability of the transcription machinery to associate with the promoter in chromatin, we found that heat shock factor, a crucial regulator of heat shock gene transcription, profited most from histone acetylation. These experiments demonstrate that histone acetylation can modulate activator access to their target sites in chromatin, and provide a causal link between histone acetylation and enhanced transcription initiation of RNA pol II in chromatin.

High resolution microanalysis and three-dimensional nucleosome structure associated with transcribing chromatin

The nucleosome is the ubiquitous and fundamental DNA-protein complex of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Biophysical studies have implicated changes in nucleosome structure from chromatin that is quiescent to active in transcription. Since DNA within the nucleosome contains a high concentration of phosphorus whereas histone proteins do not, the nucleosome structure is amenable to microanalytical electron energy loss mapping of phosphorus to delineate the DNA within the protein-nucleic acid particle. Nucleosomes associated with transcriptionally active genes were separated from nucleosomes associated with quiescent genes using mercury-affinity chromatography. The three-dimensional image reconstruction methods for the total nucleosome structure and for the 3D DNA-phosphorus distribution combined quaternion-assisted angular reconstitution of sets of single particles at random orientations and electron spectroscopic imaging. The structure of the active nucleosome has the conformation of an open clam-shell, C- or U-shaped in one view, elongated in another, and exhibits a protein asymmetry. A three-dimensional phosphorus map reveals a conformational change in nucleosomal DNA compared to DNA in the canonical nucleosome structure. It indicates an altered superhelicity and is consistent with unfolding of the particle. The results address conformational changes of the nucleosome and provide a direct structural linkage to biochemical and physiological changes which parallel gene expression.

Electrostatic contribution to the bending of DNA

A model is derived that accounts for the short-range electrostatic contribution to the bending of DNA molecule in solution and in complexes with proteins in terms of the non-linear Poisson-Boltzmann equation. We defined that the short-range electrostatic interactions depend on the changes of the polyion surface charge density under deformation, while the long-range interactions depend on the bending-induced changes in distances between each two points along the polyion axis. After an appropriate simplification of the Poisson-Boltzmann equation, the short-range term is calculated separately giving the lower limit for the electrostatic contribution to the DNA persistence length. The result is compared with the theoretical approaches developed earlier [M. Fixman, J. Chem. Phys. 76 (1982) 6346; M. Le Bret, J. Chem. Phys. 76 (1982) 6243] and with the experimental data. The conclusion is made that the results of Fixman-Le Bret, which took into account both types of the electrostatic interactions for a uniformly bent polyion, give the upper limit for the electrostatic persistence length at low ionic strength, and the actual behavior of the DNA persistence length lies between two theoretical limits. Only the short-range term is significant at moderate-to-high ionic strength where our results coincide with the predictions of Fixman-Le Bret. The bending of DNA on the protein surface that is accompanied by an asymmetric neutralization of the DNA charge is also analyzed. In this case, the electrostatic bending energy gives a significant favorite contribution to the total bending energy of DNA. Important implications to the mechanisms of DNA-protein interactions, particularly in the nucleosome particle, are discussed.

The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core

Each of the core histone proteins within the nucleosome has a central "structured" domain that comprises the spool onto which the DNA superhelix is wrapped and an N-terminal "tail" domain in which the structure and molecular interactions have not been rigorously defined. Recent studies have shown that the N-terminal domains of core histones probably contact both DNA and proteins within the nucleus and that these interactions play key roles in the regulation of nuclear processes (such as transcription and replication) and are critical in the formation of the chromatin fiber. An understanding of these complex mechanisms awaits identification of the DNA or protein sites within chromatin contacted by the tail domains. To this end, we have developed a site-specific histone protein-DNA photocross-linking method to identify the DNA binding sites of the N-terminal domains within chromatin complexes. With this approach, we demonstrate that the N-terminal tail of H2A binds DNA at two defined locations within isolated nucleosome cores centered around a position approximately 40 bp from the nucleosomal dyad and that this tail probably adopts a defined structure when bound to DNA.

Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA

The influence of ionic strength on DNA-histone and histone-histone interactions in reconstituted nucleosomes was studied by measuring the parameters of histone tyrosine fluorescence: fluorescence intensity and lambda(max) position. The first parameter is sensitive to histone-DNA interactions. The changes of the second one accrue due to hydrogen bond formation/disruption between tyrosines in the histone H2A-H2B dimer and the (H3-H4)2 tetramer. The simultaneous measurement of these parameters permits the recording of both the dissociation of histone complexes from DNA, as well as changes in histone-histone interactions. As ionic strength is increased, the H2A-H2B histone dimer dissociated first, followed by dissociation of the (H3-H4)2 tetramer [Yager, T.G., McMurray, C.T. and Van Holde, K.E. (1989) Biochemistry 28, 2271-2276]. The H2A-H2B dimer is dissociated in two stages: first, the ionic bonds with DNA were disrupted, followed by the dissociation of the histone dimer from the tetramer. And secondly, the disruption of dimer-tetramer specific H-bonds. It was established that the energy of electrostatic interactions of the histone dimer with DNA within the nucleosome is much less than the energy of interaction of the histone dimer with the tetramer.

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.

Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms

Defined oligonucleosome model systems have been used to investigate the molecular mechanisms through which the core histone tail domains modulate chromatin structure. In low salt conditions, the tail domains function at the nucleosome level to facilitate proper organization of nucleosomal DNA, i.e. wrapping of DNA around the histone octamer. Mg2+ ions can substitute for the tail domains to yield a trypsinized oligonucleosome structure that is indistinguishable from that of an intact nucleosomal array in low salt. However, Mg(2+)-dependent formation of highly folded oligonucleosome structures absolutely requires the histone tail domains, and is associated with rearrangement of the tails to a non-nucleosomal location. We conclude that the tail domains mediate oligonucleosome folding and nucleosomal DNA organization through fundamentally different molecular mechanisms.

Transcription factor-mediated chromatin remodelling: mechanisms and models

The association of DNA with nucleosomes in chromatin severely restricts the access of the regulatory factors that bring about transcription. In vivo active promoters are characterised by altered, almost transparent chromatin structures that allow the interaction of the transcriptional machinery. Recently, enzymatic activities have been discovered that facilitate the binding of transcription factors to chromatin by modifying nucleosomal structures in a process that requires energy. The mechanisms by which chromatin is remodelled may involve nucleosome movements, their transient unfolding, their partial or even complete disassembly. The dynamic properties of chromatin that underlie these structural changes are fundamental to the process of regulated gene expression.

Effects of histone acetylation, ubiquitination and variants on nucleosome stability

The properties of the nucleosomes of a salt-soluble, transcriptionally active gene-enriched fraction of chicken erythrocyte chromatin were evaluated by hydroxyapatite dissociation chromatography. We have demonstrated previously that the salt-soluble, transcriptionally active gene-enriched polynucleosomes are enriched in dynamically acetylated and ubiquitinated histones, and in an atypical U-shaped nucleosome that possessed about 20% less protein than a typical nucleosome. Further, newly synthesized histones H2A and H2B exchange preferentially with the nucleosomal histones H2A and H2B of this salt-soluble chromatin fraction. Analysis of the histones eluting from the hydroxyapatite-bound chromatin demonstrated that hyperacetylated and ubiquitinated (u), including multi-ubiquitinated, H2A-H2B.1 dimers dissociated at lower concentrations of NaCl than unmodified dimers or dimers with histone variants H2A.Z and/or H2B.2. Cross-linking studies revealed that at least 50% of uH2B.1 was paired with uH2A. uH2A-uH2B.1 dimers dissociated at lower NaCl concentrations than H2A-uH2B.1 dimers. Hyperacetylated histone (H3-H4)2 tetramers also eluted at lower concentrations of NaCl than unmodified tetramers. Our results support the idea that acetylation and ubiquitination of histones H2A and H2B.1 increase the lability of H2A-H2B.1 dimers in transcriptionally active nucleosomes. In contrast, our observations suggest that histone variants H2A.Z and H2B.2. stabilize the association of the H2A-H2B dimer in nucleosomes. The elevated lability of the H2A-H2B dimer may facilitate processes such as the exchange of these dimers with newly synthesized histones, the elongation process of transcription and transcription factor binding.

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.

Role of individual histone tyrosines in the formation of the nucleosome complex

We have determined the accessibility of histone tyrosine residues to react with p-nitrobenzenesulfonyl fluoride (NBSF) in intact nuclei, salt-dissociated nucleosomes, isolated histone complexes, and individual core histones. Of the 15 core histone tyrosine residues, 13 are inaccessible in native nucleosomes; only Tyr121 near the C-terminus of H2B is fully accessible, and Tyr54 of H3 is partially accessible under near-physiological conditions. When H1 and the basic N-terminal tails of the core histones are dissociated from the DNA by treating nuclei with 0.4 and 0.8 M NaCl, the two tyrosines which are adjacent to the basic regions of H2B and H3 become accessible as well. This indicates that these tyrosine residues may be involved in histone-DNA interactions, either directly or indirectly. When the H2A-H2B dimers are dissociated from the chromatin by raising the NaCl concentration to 1.2 M, three to four tyrosines located in the structured regions of H2B and H4 are exposed, suggesting that these tyrosine residues may be located at the dimer-tetramer interface. Dissociating all the histones from the DNA at an even higher ionic strength as a mixture of dimers, tetramers, and octamers does not change the pattern of Tyr exposure, but reduces the reactivity of the tyrosines at the dimer-tetramer interface as would be expected from the reassociation of H2A-H2B dimers and H3-H4 tetramers.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of the changes in the structure and hydration of the nucleosome core particle at moderate ionic strengths

In order to better understand the conformational changes induced in the nucleosome core particle by changes in the ionic strength of the media in the range from 0.1 to 0.6 M NaCl, we have conducted a very detailed structural analysis, combining circular dichroism, DNase I digestion, and sedimentation equilibrium. The results of such analysis indicate that the secondary structure of both DNA and histones exhibits small (approximately 5%) but noticeable changes as the salt increases within this range. In the case of DNA, the data are consistent with a trend toward a more relaxed secondary structure. The DNase I pattern of digestion is also altered by the salt and suggests a DNA relaxation around the flanking ends. From the hydrodynamic measurements, we also observe a significant change in the virial coefficients of the particle as the salt increases, which in turn are in very good agreement with the theoretically expected values. Furthermore, the preferential hydration parameter is also found to increase with the salt. We believe that the self-dependent conformational change of the nucleosome core particle is the result of the conjunction of all these subtle changes. Yet, from the present data, their exact relationship to the tertiary structure of the whole particle at the different ionic strengths cannot be exactly defined.

Irreversible changes occur in chromatin structure upon dissociation of histone H1

The role of histone H1 in the actual interactions bringing about chromatin folding is investigated by studying the reversibility of its dissociation. H1 was dissociated by increase of the NaCl concentration and reassociated by dialysis, without removal from the dialysis bag. To scrutinize the fidelity of this stoichiometric form of chromatin reconstitution, we use circular dichroism, nuclease digestion, thermal denaturation and the sensitive electric birefringence method. No alteration of the repeat length and no nucleosomal sliding are observed upon the reassociation procedure. However, under all the different conditions investigated, the original value of the positive electric birefringence is never recovered, indicating an irreversible change of structure. CD and melting profiles confirm that DNA-protein interactions are modified, and orientational relaxation time measurements indicate that these structural perturbations affect the salt-induced transition of polynucleosomal fibers. The striking conclusion of these studies is that variations of ionic concentration are sufficient to induce irreversible structural alterations affecting the higher-order folding of chromatin. It is of interest that the only sample which exhibits behavior upon reassociation comparable to that of native chromatin is the one which experienced the fastest salt transitions. We suggest that these conformational changes arise from the unbinding to DNA of certain basic tails of histone(s), and that a competition for DNA binding locations exists upon the reassociation. These results are then additional arguments (Mazen, A., Hacques, M.F. and Marion, C.,J. Mol. Biol. 194, 741-745 (1987)), to suggest that dissociation of H1 might modify a direct interaction between basic tails of core histones and H1.

A NMR study of mobility in the histone octamer

The histone octamer from chicken erythrocytes was studied in 2 M NaCl using 500 mHz 1H NMR spectroscopy. We compared the spectrum of control octamers with that of octamers isolated from trypsinized nucleosome core particles. We observe that the sharp resonances found in the spectrum of the native octamer disappear completely after trypsinization. Therefore, within the time frame of the NMR experiment, all of the mobile amino acid residues in the histone octamer are found in the well defined trypsin sensitive domains. These results indicate that there is a very clear structural demarcation between the random coil N- and C-terminal tails and the globular domains of the histones.

H3 Cys-110 is in close proximity to the C-terminal regions of H2B and H4 in a nucleosome core with an altered internal arrangement of histones

A particle obtained by nuclease digestion of nucleohistone complexes prepared by direct mixing of histones with DNA in 0.15 M NaCl was indistinguishable by composition and physical properties from nucleosome cores prepared under the same conditions from nucleohistone preannealed in 0.6 M NaCl. We show here that different photo-cross-links form when these particles are prepared from H3 labeled with photoaffinity reagents on the unique histone H3 cysteine. H3-H3 histone dimers were dominant when the particles were prepared by dilution of the nucleohistone from 0.6 M NaCl while H3-H2B and H3-H4 histone dimers were prominent if the nucleohistone complex was prepared directly in 0.15 M NaCl. Peptide mapping of the novel H3-H4 and H3-H2B dimers showed that Cys-110 of histone H3 is cross-linked to the 18 amino acid C-terminal end of H4 or to the 66 amino acid C-terminal half of H2B.

Electrostatic mechanism of chromatin folding

We describe a theoretical analysis of cation binding in the nucleosome, and in chromatin as it folds, using Manning's polyelectrolyte theory. The theory accounts remarkably well, even quantitatively, both for the interaction of histone charges with DNA in chromatin, and for the essential features of the folding process. The degree of chromatin folding under different ion conditions is reliably predicted by the electrostatic free energy of DNA in the H1 binding site, which determines repulsions between linker DNA segments thus limiting how closely they may approach. The electrostatic free energy is a function of the ionic strength and the residual (unneutralized) DNA charge. Monovalent cations effect chromatin folding primarily by screening the residual charge whilst divalent or trivalent cations bind to DNA reducing its residual charge. The binding of H1 to the linker DNA considerably reduces its electrostatic free energy by displacing bound cations and reducing the residual charge. Thus, native chromatin folds at lower salt concentrations than does H1-depleted chromatin. We conclude that the mechanism of chromatin folding is primarily electrostatic in nature. In vivo ion conditions are such that chromatin is compact but H1 molecules are able to exchange freely, probably due to a low degree of salt-induced dissociation. When H1 molecules exchange, transient local disruptions may occur in the chromatin filament due to repulsion of temporarily H1-free linker DNA from within the filament, such that chromatin "breathes". Thus, the cell can maintain its chromatin in a compact form and access to DNA for sequence-specific DNA-binding proteins and the transcription machinery is still possible.

Laser-induced crosslinking of histones to DNA in chromatin and core particles: implications in studying histone-DNA interactions

UV laser irradiation has been used to covalently crosslink histones to DNA in nuclei, chromatin and core particles and the presence of the different histone species in the covalently linked material was detected immunochemically. When nuclei were irradiated and then trypsinized to cleave the N- and C- terminal histone tails, no histones have been found covalently linked to DNA. This finding shows that UV laser-induced crosslinking of histones to DNA is accomplished via the non-structured domains only. This unexpected way of crosslinking operated in chromatin, H1-depleted chromatin and core particles, i.e. independently of the chromatin structure. The efficiency of crosslinking, however, showed such a dependence: whilst the yield of crosslinks was similar in total and H1-depleted chromatin, in core particles the efficiency was 3-4 times lower for H2A, H2B and H4 and 10-12 times lower for H3. The decreased crosslinking efficiency, especially dramatic in the case of H3, is attributed to a reduced number of binding sites, and, respectively, is considered as a direct evidence for interaction of nonstructured tails of core histones with linker DNA.

Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome

Using immobilized trypsin and an appropriate fractionation procedure, we have been able to prepare, for the first time, nucleosome core particles containing selectively trypsinized histone domains. The particles thus obtained: [(H3T-H4T)2-2(H2AT-H2BT)].DNA; [(H3-H4)2-2(H2AT-H2BT)].DNA; [H3T-H4T)2-2(H2A-H2B)].DNA (where T means trypsinized), together with the non-trypsinized controls have been characterized using the following techniques: analytical ultracentrifugation, circular dichroism, thermal denaturation and DNAse I digestion. The major aim of this study was to analyze the role of the amino-terminal regions (the histone "tails") on the stability of the nucleosome in solution. The data obtained from this analysis clearly show that stability of the nucleosome core particle to dissociation (below a salt concentration of 0.7 M-NaCl) is not affected by the presence or the absence of any of the N-terminal regions of the histones. Furthermore, these histone regions make very little contribution, if any, to the conformational transition that nucleosomes undergo in this range of salt concentrations. They play, however, a very important role in determining the thermal stability of the particle, as reflected in the dramatic alterations exhibited by the melting profiles upon selective removal of these tails by trypsinization. The melting data can be explained by a simple hypothesis that ascribes interaction of H2A/H2B and H3/H4 tails to particular regions of the nucleosomal DNA.