On the Mechanism of Nucleosome Assembly by Histone Chaperone NAP1

The activity of the histone chaperone yeast Asf1 in the assembly and disassembly of histone H3/H4-DNA complexes

The deposition of the histones H3/H4 onto DNA to give the tetrasome intermediate and the displacement of H3/H4 from DNA are thought to be the first and the last steps in nucleosome assembly and disassembly, respectively. Anti-silencing function 1 (Asf1) is a chaperone of the H3/H4 dimer that functions in both of these processes. However, little is known about the thermodynamics of chaperone–histone interactions or the direct role of Asf1 in the formation or disassembly of histone–DNA complexes. Here, we show that Saccharomyces cerevisiae Asf1 shields H3/H4 from unfavorable DNA interactions and aids the formation of favorable histone–DNA interactions through the formation of disomes. However, Asf1 was unable to disengage histones from DNA for tetrasomes formed with H3/H4 and strong nucleosome positioning DNA sequences or tetrasomes weakened by mutant (H3K56Q/H4) histones or non-positioning DNA sequences. Furthermore, Asf1 did not associate with preformed tetrasomes. These results are consistent with the measured affinity of Asf1 for H3/H4 dimers of 2.5 nM, which is weaker than the association of H3/H4 for DNA. These studies support a mechanism by which Asf1 aids H3/H4 deposition onto DNA but suggest that additional factors or post-translational modifications are required for Asf1 to remove H3/H4 from tetrasome intermediates in chromatin.

A coupled equilibrium approach to study nucleosome thermodynamics

The repeating structural unit of eukaryotic chromatin, the nucleosome, is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. These proteins form an octamer around which 147bp of DNA is wrapped in 1.65 superhelical turns (Luger et al., 1997). The nucleosome represents a major obstacle for any protein seeking access to the DNA. Several strategies have evolved to regulate access to nucleosomal DNA, such as posttranslational modification of histones and histone variants, ATP-dependent chromatin remodeling machines, and histone chaperones. It is likely that most if not all of these mechanisms directly impact the thermodynamics of the nucleosome. The DNA sequence itself may also impact its own inherent accessibility through modulating nucleosome positioning and/or thermodynamics. However, these working hypotheses could not be tested directly because no assays to measure nucleosome stability under physiological conditions were available. Attempts to determine the stability of nucleosomes have been hampered by the fact that the nucleosomes do not assemble in vitro under physiological conditions, but will only form nucleosomes through titration from high (2M) to low (>0.3M) ionic strength. We have developed a coupled equilibrium approach using the histone chaperone Nap1 to measure nucleosome thermodynamics under physiological conditions. This method will be useful for examining the impact of DNA sequence, histone variants, and posttranslational modifications on nucleosome thermodynamics.

Statistical-mechanical lattice models for protein-DNA binding in chromatin

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibria measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical-mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.

Nucleoplasmin binds histone H2A-H2B dimers through its distal face

Nucleoplasmin (NP) is a pentameric chaperone that regulates the condensation state of chromatin extracting specific basic proteins from sperm chromatin and depositing H2A-H2B histone dimers. It has been proposed that histones could bind to either the lateral or distal face of the pentameric structure. Here, we combine different biochemical and biophysical techniques to show that natural, hyperphosphorylated NP can bind five H2A-H2B dimers and that the amount of bound ligand depends on the overall charge (phosphorylation level) of the chaperone. Three-dimensional reconstruction of NP/H2A-H2B complex carried out by electron microscopy reveals that histones interact with the chaperone distal face. Limited proteolysis and mass spectrometry indicate that the interaction results in protection of the histone fold and most of the H2A and H2B C-terminal tails. This structural information can help to understand the function of NP as a histone chaperone.

The histone shuffle: histone chaperones in an energetic dance

Our genetic information is tightly packaged into a rather ingenious nucleoprotein complex called chromatin in a manner that enables it to be rapidly accessed during genomic processes. Formation of the nucleosome, which is the fundamental unit of chromatin, occurs via a stepwise process that is reversed to enable the disassembly of nucleosomes. Histone chaperone proteins have prominent roles in facilitating these processes as well as in replacing old histones with new canonical histones or histone variants during the process of histone exchange. Recent structural, biophysical and biochemical studies have begun to shed light on the molecular mechanisms whereby histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription.

Structure, localization and histone binding properties of nuclear-associated nucleosome assembly protein from Plasmodium falciparum

BACKGROUND

Nucleosome assembly proteins (NAPs) are histone chaperones that are crucial for the shuttling and incorporation of histones into nucleosomes. NAPs participate in the assembly and disassembly of nucleosomes thus contributing to chromatin structure organization. The human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS.

METHODS

Three-dimensional crystal structure of PfNapS has been determined and analysed. Gene knockout and localization studies were also performed on PfNapS using transfection studies. Fluorescence spectroscopy was performed to identify histone-binding sites on PfNapS. Extensive sequence and structural comparisons were done with the crystal structures available for NAP/SET family of proteins.

RESULTS

Crystal structure of PfNapS shares structural similarity with previous structures from NAP/SET family. Failed attempts to knock-out the gene for PfNapS from malaria parasite suggest essentiality in the parasite. GFP-fused PfNapS fusion protein targeting indicates cellular localization of PfNapS in the parasite nucleus. Fluorescence spectroscopy data suggest that PfNapS interacts with core histones (tetramer, octamer, H3, H4, H2A and H2B) at a different site from its interaction with linker histone H1. This analysis illustrates two regions on the PfNapS dimer as the possible sites for histone recognition.

CONCLUSIONS

This work presents a thorough analysis of the structural, functional and regulatory attributes of PfNapS from P. falciparum with respect to previously studied histone chaperones.

The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions

The organization of the eukaryotic genome into nucleosomes dramatically affects the regulation of gene expression. The delicate balance between transcription and DNA compaction relies heavily on nucleosome dynamics. Surprisingly, little is known about the free energy required to assemble these large macromolecular complexes and maintain them under physiological conditions. Here, we describe the thermodynamic parameters that drive nucleosome formation in vitro. To demonstrate the versatility of our approach, we test the effect of DNA sequence and H3K56 acetylation on nucleosome thermodynamics. Furthermore, our studies reveal the mechanism of action of the histone chaperone nucleosome assembly protein 1 (Nap1). We present evidence for a paradigm in which nucleosome assembly requires the elimination of competing, nonnucleosomal histone-DNA interactions by Nap1. This observation is confirmed in vivo, wherein deletion of the NAP1 gene in yeast results in a significant increase in atypical histone-DNA complexes, as well as in deregulated transcription activation and repression.

Nucleosome formation activity of human somatic nuclear autoantigenic sperm protein (sNASP)

NASP (nuclear autoantigenic sperm protein) is a member of the N1/N2 family, which is widely conserved among eukaryotes. Human NASP reportedly prefers to bind to histones H3.H4 and the linker histone H1, as compared with H2A.H2B, and is anticipated to function as an H3.H4 chaperone for nucleosome assembly. However, the direct nucleosome assembly activity of human NASP has not been reported so far. In humans, two spliced isoforms, somatic and testicular NASPs (sNASP and tNASP, respectively) were identified. In the present study we purified human sNASP and found that sNASP efficiently promoted the assembly of nucleosomes containing the conventional H3.1, H3.2, H3.3, or centromere-specific CENP-A. On the other hand, sNASP inefficiently promoted nucleosome assembly with H3T, a testis-specific H3 variant. Mutational analyses revealed that the Met-71 residue of H3T is responsible for this inefficient nucleosome formation by sNASP. Tetrasomes, composed of the H3.H4 tetramer and DNA without H2A.H2B, were efficiently formed by the sNASP-mediated nucleosome-assembly reaction. A deletion analysis of sNASP revealed that the central region, amino acid residues 26-325, of sNASP is responsible for nucleosome assembly in vitro. These experiments are the first demonstration that human NASP directly promotes nucleosome assembly and provide compelling evidence that sNASP is a bona fide histone chaperone for H3.H4.

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4(+) T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.

New developments in post-translational modifications and functions of histone H2A variants

Structural variability within histone families, such as H2A, can be achieved through 2 primary mechanisms: the expression of histone variants and the incorporation of chemical modifications. The histone H2A family contains several variants in addition to the canonical H2A forms. In this review, recent developments in the study of the heteromorphous variants H2A.X, H2A.Z, and macroH2A will be discussed. Particular focus will be given to the post-translational modifications (PTMs) of these variants, including phosphorylation, ubiquitination, acetylation, and methylation. The combination of the newly identified N- and C-terminal tail PTMs expands the multiplicity of roles that the individual H2A variants can perform. It is of additional interest that analogous sites within these different histone variants can be similarly modified. Whether this is a redundant function or a finely tuned one, designed to meet specific needs, remains to be elucidated.

Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative characterisation of the interaction

BACKGROUND

The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Ibeta belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Ibeta, we designed several SET/TAF-Ibeta truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays.

RESULTS

Wild type SET/TAF-Ibeta binds to histones H2B and H3 with Kd values of 2.87 and 0.15 microM, respectively. The preferential binding of SET/TAF-Ibeta to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Ibeta, as well as the H3 amino-terminal tail, are dispensable for this interaction.

CONCLUSION

This type of analysis allowed us to assess the relative affinities of SET/TAF-Ibeta for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Ibeta and can be valuable to understand the role of SET/TAF-Ibeta in chromatin function.

A thermodynamic model for Nap1-histone interactions

The yeast nucleosome assembly protein 1 (yNap1) plays a role in chromatin maintenance by facilitating histone exchange as well as nucleosome assembly and disassembly. It has been suggested that yNap1 carries out these functions by regulating the concentration of free histones. Therefore, a quantitative understanding of yNap1-histone interactions also provides information on the thermodynamics of chromatin. We have developed quantitative methods to study the affinity of yNap1 for histones. We show that yNap1 binds H2A/H2B and H3/H4 histone complexes with low nm affinity, and that each yNap1 dimer binds two histone fold dimers. The yNap1 tails contribute synergistically to histone binding while the histone tails have a slightly repressive effect on binding. The (H3/H4)(2) tetramer binds DNA with higher affinity than it binds yNap1.

ATP-dependent chromatosome remodeling

Chromatin serves to package, protect and organize the complex eukaryotic genomes to assure their stable inheritance over many cell generations. At the same time, chromatin must be dynamic to allow continued use of DNA during a cell's lifetime. One important principle that endows chromatin with flexibility involves ATP-dependent 'remodeling' factors, which alter DNA-histone interactions to form, disrupt or move nucleosomes. Remodeling is well documented at the nucleosomal level, but little is known about the action of remodeling factors in a more physiological chromatin environment. Recent findings suggest that some remodeling machines can reorganize even folded chromatin fibers containing the linker histone H1, extending the potential scope of remodeling reactions to the bulk of euchromatin.

Acetylation of H4 suppresses the repressive effects of the N-termini of histones H3/H4 and facilitates the formation of positively coiled DNA

We have studied the role of the N-termini of histones H3/H4 in the regulation of the conformational changes that occur in H3/H4 during their deposition on DNA by NAP1 (nucleosome assembly protein 1). Removal of the N-termini extensively increased the right-handed conformation of H3/H4 as assayed by the increased levels of positive coils that were formed on DNA. The osmolytes, TMAO, betaine, sarcosine, alanine, glycine, and proline to varying degrees, facilitated the formation of positive coils. The denaturant, urea (0.6 M), blocked the osmolyte effects, causing a preference of H3/H4 to form negative coils (the left-handed conformation). Acetylated H3/H4 also formed high levels of positive coils, and it is proposed that both the osmolytes and acetylation promote the formation of an alpha-helix in the N-termini. This structural change may ultimately explain a unique feature of transcription through nucleosomes, i.e., that H2A/H2B tends to be more mobile than H3/H4. By using combinations of H3 and H4 that were either acetylated or the N-termini removed, it was also determined that the N-terminus of H4 is primarily responsible for repressing the formation of positive coils. Additional gradient analyses indicate that NAP1 establishes an equilibrium with the H3/H4-DNA complexes. This equilibrium facilitates a histone saturation of the DNA, a unique state that promotes the right-handed conformation. NAP1 persists in the binding of the complexes through interaction with the N-terminus of H3, which may be a mechanism for subsequent remodeling of the nucleosome during transcription and replication.

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro

Five non-allelic histone H3 variants, H3.1, H3.2, H3.3, H3t and CENP-A, have been identified in mammals. H3t is robustly expressed in the testis, and thus was assigned as the testis-specific H3 variant. However, recent proteomics and tissue-specific RT-PCR experiments revealed a small amount of H3t expression in somatic cells. In the present study, we purified human H3t as a recombinant protein, and showed that H3t/H4 forms nucleosomes with H2A/H2B by the salt-dialysis method, like the conventional H3.1/H4. We found that H3t/H4 is not efficiently incorporated into the nucleosome by human Nap1 (hNap1), due to its defective H3t/H4 deposition on DNA. In contrast, human Nap2 (hNap2), a paralog of hNap1, promotes nucleosome assembly with H3t/H4. Mutational analyses revealed that the Ala111 residue, which is conserved among H3.1, H3.2 and H3.3, but not in H3t, is the essential residue for the hNap1-mediated nucleosome assembly. These results suggest that H3t may be incorporated into chromatin by a specific chaperone-mediated pathway.

Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation

Based on model structures with atomic resolution, a coarse-grained model for the nucleosome geometry was implemented. The dependence of the chromatin fiber conformation on the spatial orientation of nucleosomes and the path and length of the linker DNA was systematically explored by Monte Carlo simulations. Two fiber types were analyzed in detail that represent nucleosome chains without and with linker histones, respectively: two-start helices with crossed-linker DNA (CL conformation) and interdigitated one-start helices (ID conformation) with different nucleosome tilt angles. The CL conformation was derived from a tetranucleosome crystal structure that was extended into a fiber. At thermal equilibrium, the fiber shape persisted but relaxed into a structure with a somewhat lower linear mass density of 3.1 +/- 0.1 nucleosomes/11 nm fiber. Stable ID fibers required local nucleosome tilt angles between 40 degrees and 60 degrees. For these configurations, much higher mass densities of up to 7.9 +/- 0.2 nucleosomes/11 nm fiber were obtained. A model is proposed, in which the transition between a CL and ID fiber is mediated by relatively small changes of the local nucleosome geometry. These were found to be in very good agreement with changes induced by linker histone H1 binding as predicted from the high resolution model structures.

NAP1 catalyzes the formation of either positive or negative supercoils on DNA on basis of the dimer-tetramer equilibrium of histones H3/H4

We have studied the tetramer-dimer equilibrium of histones H3/H4 and its effect on DNA supercoiling. Two approaches were found to shift the equilibrium toward dimer. In both instances, when deposited on DNA, the dimers formed positively coiled DNA. The first approach was to modify cysteine 110 of H3 with 5,5'-dithio-bis(2-nitrobenzoic acid (DTNB) and to directly add the histones to DNA at physiological ionic strength. The second approach involved adding an excess of the histone chaperone, nucleosome assembly protein 1 (NAP1) to the H3/H4 prior to deposition on the DNA. It was also observed that when H3/H4 were deposited in the tetrameric state, negatively coiled DNA was formed. The topological state of the DNA prior to deposition was also found to influence the final conformational state of H3/H4. It is proposed that in the tetrameric state, the H3-H3 interface has a left-handed pitch prior to binding DNA. In the dimeric state, the H3-H3 interface is not established until bound to DNA, at which point either the left or right-handed pitch will form on the basis of the initial topology of the DNA. Formaldehyde cross-linking and reversal were applied to identify the histone-histone interactions that facilitate the formation of positive stress. Higher-order interactions between multiple H3/H4 dimers were required to propagate this specific conformation. Changes in the conformational state of H3/H4 were also observed when the histones were bound to DNA prior to treatment with NAP1. It is proposed that these conformational changes in H3/H4 are involved in promoter activation and transcription elongation through nucleosomes.

Protein-protein Förster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z

A protein-protein Förster resonance energy transfer (FRET) system, employing probes at multiple positions, was designed to specifically monitor the dissociation of the H2A-H2B dimer from the nucleosome core particle (NCP). Tryptophan donors and Cys-AEDANS acceptors were chosen because, compared to previous NCP FRET fluorophores, they: (1) are smaller and less hydrophobic, which should minimize perturbations of histone and NCP structure; and (2) have an R0 of 20 A, which is much less than the dimensions of the NCP (approximately 50 A width and approximately 100 A diameter). Equilibrium protein unfolding titrations indicate that the donor and acceptor moieties have minimal effects on the stability of the H2A-H2B dimer and (H3-H4)2 tetramer. NCPs containing the various FRET pairs were reconstituted with the 601 DNA positioning element. Equilibrium NaCl-induced dissociation of the modified NCPs showed that the 601 sequence stabilized the NCP to dimer dissociation relative to weaker positioning sequences. This finding implies a significant role for the H2A-H2B dimers in determining the DNA sequence dependence of NCP stability. The free energy of dissociation determined from reversible and well-defined sigmoidal transitions revealed two distinct phases reflecting the dissociation of individual H2A-H2B dimers, confirming cooperativity as suggested previously; these data allow quantitative description of the cooperativity. The FRET system was then used to study the effects of the histone variant H2A.Z on NCP stability; previous studies have reported both destabilizing and stabilizing effects. H2A.Z FRET NCP dissociation transitions suggest a slight increase in stability but a significant increase in cooperativity of the dimer dissociations. Thus, the utility of this protein-protein FRET system to monitor the effects of histone variants on NCP dynamics has been demonstrated, and the system appears equally well-suited for dissection of the kinetic processes of dimer association and dissociation from the NCP.

CENP-A-containing nucleosomes: easier disassembly versus exclusive centromeric localization

CENP-A is a histone variant that replaces conventional H3 in nucleosomes of functional centromeres. We report here, from reconstitutions of CENP-A- and H3-containing nucleosomes on linear DNA fragments and the comparison of their electrophoretic mobility, that CENP-A induces some positioning of its own and some unwrapping at the entry-exit relative to canonical nucleosomes on both 5 S DNA and the alpha-satellite sequence on which it is normally loaded. This steady-state unwrapping was quantified to 7(+/-2) bp by nucleosome reconstitutions on a series of DNA minicircles, followed by their relaxation with topoisomerase I. The unwrapping was found to ease nucleosome invasion by exonuclease III, to hinder the binding of a linker histone, and to promote the release of an H2A-H2B dimer by nucleosome assembly protein 1 (NAP-1). The (CENP-A-H4)2 tetramer was also more readily destabilized with heparin than the (H3-H4)2 tetramer, suggesting that CENP-A has evolved to confer its nucleosome a specific ability to disassemble. This dual relative instability is proposed to facilitate the progressive clearance of CENP-A nucleosomes that assemble promiscuously in euchromatin, especially as is seen following CENP-A transient over-expression.

The nucleosome assembly activity of NAP1 is enhanced by Alien

The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitamin D receptor (VDR), binds in vivo and in vitro to NAP1 and modulates its activity by enhancing NAP1-mediated nucleosome assembly on DNA. Furthermore, Alien reduces the accessibility of the histones H3 and H4 for NAP1-promoted assembly reaction. This indicates that Alien sustains and reinforces the formation of nucleosomes. Employing deletion mutants of Alien suggests that different regions of Alien are involved in enhancement of NAP1-mediated nucleosome assembly and in inhibiting the accessibility of the histones H3 and H4. In addition, we provide evidence that Alien is associated with chromatin and with micrococcus nuclease-prepared nucleosome fractions and interacts with the histones H3 and H4. Furthermore, chromatin immunoprecipitation and reimmunoprecipitation experiments suggest that NAP1 and Alien localize to the endogenous CYP24 promoter in vivo, a VDR target gene. Based on these findings, we present here a novel pathway linking corepressor function with nucleosome assembly activity.

Nap1: taking a closer look at a juggler protein of extraordinary skills

The nucleosome assembly protein Nap1 is used extensively in the chromatin field to reconstitute nucleosomal templates for structural and functional studies. Beyond its role in facilitating experimental investigation of nucleosomes, the highly conserved Nap1 is one of the best-studied members of the histone chaperone group. Here we review its numerous functions, focusing mainly on its roles in assembly and disassembly of the nucleosome particle, and its interactions with chromatin remodeling factors. Its presumed role in transcription through chromatin is also reviewed in detail. An attempt is made to clearly discriminate between fact and fiction, and to formulate the unresolved questions that need further attention. It is beyond doubt that the numerous, seemingly unrelated functions of this juggler protein have to be precisely channeled, coordinated, and regulated. Why nature endowed this specific protein with so many functions may remain a mystery. We are aware of the enormous challenge to the scientific community that understanding the mechanisms underlying these activities presents.

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.

Transcription elongation through a chromatin template

DNA transaction events occurring during cell life (replication, transcription, recombination, repair, cell division) are always linked to severe changes in the topological state of the double helix. However, since naked DNA almost does not exist in eukaryote nucleus but rather interacts with various proteins, including ubiquitous histones, these topological changes happen in a chromatin context. This review focuses on the role of chromatin fiber structure and dynamics in the regulation of transcription, with an almost exclusive emphasis on the elongation step. Beside a brief overview of our knowledge about transcribed chromatin, we will see how recent mechanistic and biochemical studies give us new insights into the way cell could modulate DNA supercoiling and chromatin conformational dynamics. The participation of topoisomerases in this complex ballet is discussed, since recent data suggest that their role could be closely related to the precise chromatin structure. Lastly, some future prospects to carry on are proposed, hoping this review will help in stimulating discussions and further investigations in the field.