Flexibility Of Nucleosomes On Topologically Constrained DNA

FLEXIBILITY OF NUCLEOSOMES ON TOPOLOGICALLY CONSTRAINED DNA ANDREI SIVOLOB∗ , CHRISTOPHE LAVELLE† , AND ARIEL PRUNELL‡ Abstract. The nucleosome plays an ever increasing role in our comprehension of the regulation of gene activity. Here we review our results on nucleosome conformational flexibility, its molecular mechanism and its functional relevance. Our initial approach combined both empirical measurement and theoretical simulation of the topological properties of single particles reconstituted on DNA minicircles. Two types of particles were studied in addition to the conventional nucleosome: a subnucleosome consisting of DNA wrapped around the (H3-H4)2 histone tetramer, now known as a tetrasome, and the linker histone H5/H1-bearing nucleosome, or chromatosome. All particles were found to thermally fluctuate between two to three conformational states, which differed by their topological and mechanical characteristics. These findings were confirmed for the nucleosome and the tetrasome by the use of magnetic tweezers to apply torsions to single arrays of these particles reconstituted on linear DNA. These latter experiments further revealed a new structural form of the nucleosome, the reversome, in which DNA is wrapped in a right-handed superhelical path around a distorted octamer. This work suggests that the single most important role of chromatin may be to considerably increase overall DNA flexibility, which might indeed be a requirement of genome function. Key words. Nucleosomes, DNA minicircles, DNA supercoiling, conformational flexibility, chiral transition, magnetic tweezers, single molecules, chromatin fibers, chromatin superstructure. AMS(MOS) subject classifications. 92C05 Biophysics, 92C40 Biochemistry, molecular biology. 1. Introduction. DNA in the cell nucleus is bound to basic proteins, the histones, to form chromatin, whose repeat unit is the nucleosome. The core of the nucleosome (the core particle) contains 147 bp of DNA wrapped in ∼1.7 turns of a left-handed superhelix around an octamer of two copies each of the four core histones H2A, H2B, H3 and H4. Its high-resolution crystallographic structure [1–4] (Fig. 1a) is characterized by a pseudo twofold axis of symmetry that passes through the H3/H3 interface (the fourhelix bundle) and the central base pair of the 147 bp DNA fragment where the major groove faces the octamer. That point is defined as superhelix location zero, SHL0, and for each successive turn of the double helix the SHL number increases positively or negatively up to ±7 (Fig. 1a). The histone octamer is tripartite, being made of a (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The (H3-H4)2 tetramer organizes the central 3/4 ∗ Department of General and Molecular Genetics, Taras Shevchenko National University, 64 Vladimirskaya street, 01033 Kiev, Ukraine ([email protected]). † Laboratoire Physico-Chimie Curie, UMR CNRS 168, Institut Curie, 11 rue P. et M. Curie, 75231 Paris Cedex 05, France ([email protected]). ‡ Former affiliation: Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Denis Diderot Paris 7 et Université P. et M. Curie Paris 6, 2 place Jussieu, 75251 Paris Cédex 05, France. ([email protected]). 251 C.J. Benham et al. (eds.), Mathematics of DNA Structure, Function and Interactions, The IMA Volumes in Mathematics and its Applications 150, DOI 10.1007/978-1-4419-0670-0_13, © Springer Science+Business Media, LLC 2009 252 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 1. 1.9 Å-resolution crystal structures. a) The 147 bp nucleosome core particle [PDB ID # 1KX5]. b) The tetrasome (central 55 bp on the (H3-H4)2 tetramer) extracted from the core particle. Numbers indicate the SHLs (SuperHelix Locations). Images were created using UCSF Chimera (http://www.cgl.ucsf.edu/chimera). turn of the superhelix in between SHL±2.5 (Fig. 1b). This subnucleosome particle, called a tetrasome, or its precursor, the hexasome, may occur transiently through H2A-H2B dimer release during nucleosome remodeling [5] and/or transcription elongation [6–10]. H2A-H2B dimers complete the nucleosome by interacting with the two distal DNA regions from SHL+3.5 to +5.5 and SHL−3.5 to −5.5. Binding of the DNA ends at SHL±6.5 to the H3 α N extensions finally seals the DNA wrapping. The specific arrangement of α-helices in each histone, called the histone fold, not only insures the above described histone-DNA interactions, but also the histonehistone interactions within the octamer. The positively charged N-terminal tails of the histones protrude out from the particle, with H2B and H3 tails passing between the two gyres of the DNA superhelix through the channels formed by the aligned minor grooves [1]. The tails of H3, which are especially long, are appropriately located to interact with nucleosome entry/exit DNAs (Fig. 1a) and reduce their electrostatic repulsion. The tails, which are the substrate for various post-translational modifications [11], may also serve as platforms for the binding of specific activities (i.e. the so-called histone-code; [12, 13]). Among the various tail modifications, acetylation of lysine residues is associated with transcriptional activation (reviewed in [14, 15]). The pleiotropic roles of the tails also appear to include the modulation of nucleosome sliding and remodeling [13, 16, 17]. FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 253 A single copy of the fifth histone, also known as the linker histone, H1 or H5 (H1 homologue in avian erythrocytes), interacts with the nucleosome. The H1/H5 molecule has an N-terminal tail, a globular domain and a long, highly positively charged, C-terminal tail (84 residues out of a total of 149 for H5) [18]. The globular domain seals the two superhelical turns at the DNA entry-exit, while the C-tail interacts further along these DNAs (see Section 2.3, below) [19–21]. The particle formed by the histone octamer, ∼166 bp of DNA, and the H1/H5 histone is the chromatosome [19]. Nucleosomes in chromatin are connected by ∼ 20–70 bp linker DNAs, resulting in an extended bead-on-a-string arrangement. This structure condenses at physiological ionic strength to resemble a zigzag by a process that is strictly dependent on the core histone tails [22–26]. At the next level of condensation, H1/H5 is required to stabilize a compact 30 nm chromatin fiber [27]. Microscopic techniques [28–30] and X-ray crystallography [31] have shown that the irregular 3D zigzag has nucleosomes with straight linkers projecting toward the fiber interior. Such a cross-linker model was also predicted by theoretical modeling [32–35], and is consistent with the internal location of H1/H5 [36–38] and the bridging together of nucleosome entry/exit DNAs into a stem through interactions with H1/H5 C-terminal tail (see Fig. 9, below) [21]. This stem could be recognized a posteriori in electron micrographs of native chromatin fragments [39] and it was subsequently considered as a unique structural motif directing chromatin higher order folding [40]. In the past decade, new concepts have emerged to illuminate the role of chromatin in regulating the access of transcriptional factors to their target sites. The central mechanism appears to be chromatin remodeling, both chemical, through covalent histone modifications (in particular acetylation; see above) and physical, whereby the energy of ATP hydrolysis is used to mobilize and structurally alter nucleosomes (reviewed in [41–45]). The latter mechanism may take advantage of inherent nucleosome dynamics, as shown by the spontaneous accessibility of nucleosomal DNA to binding proteins [46–48], and by the fluctuations of the fluorescence resonance energy transfer (FRET) between an acceptor and a donor fluorophores. These fluorophores, whose FRET efficiency is dependent on the distance, revealed dynamic modes when they were located i) either 75 bp apart in the same DNA fragment, so that DNA wrapping would bring them in register close to the dyad axis [49, 50]; ii) in the DNA and in the histones; or iii) both in the histones [48, 51, 52]. Other evidence for dynamic behavior of nucleosomes can be found in their ability to slide along the DNA at higher temperatures and salt [53], in the dependence of their overall structure on ionic strength, as again observed by FRET [50, 51], and in the extensive differences in DNA distortions observed between crystallized core particles on 146 and 147 bp of the same α-satellite sequence [1, 3]. This review is devoted to our studies of the topological manifestation of intrinsic nucleosome dynamics, which could be more relevant to their 254 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL situation in vivo. It may be that nucleosomes with free DNA ends display artificially enhanced dynamics compared to nucleosomes that usually are, like ours, topologically constrained. Our results derive from two different substrates: single particles assembled on supercoiled DNA minicircles, and nucleosome arrays reconstituted on linear DNA with both ends attached. Minicircles were relaxed with topoisomerase I, and the products were analyzed and brought to simulations. Nucleosome arrays were subjected to rotational constraints using magnetic tweezers, and their length-vs.-torsion response was used to analyze nucleosome behavior in the context of the fiber. The following sections describe the methods, the results, and their potential physiological relevance. 2. A particle on a DNA minicircle. DNA topoisomers are identified by their linking number, Lk. Lk satisfies the well-known equation [54–56]: Lk = T w + W r, (2.1) where Tw = N/h is the twist of the double helix, with N being the number of base pairs and h the helical periodicity, and Wr the writhing of the closed curve formed by the double helix axis. Note that here and below the helical periodicity h is the so-called intrinsic or twist-related helical periodicity, i.e. the periodicity of the double helix in the laboratory frame. Generally, the linking number Lk does not coincide with the most probable twist Tw 0 = Lk 0 = N/h0 , where h0 is the most probable helical periodicity for given conditions. This results in an elastic constraint in the circular DNA, which is measured by the linking number difference ∆Lk = Lk − Lk0 . (2.2) ∆Lk = ∆T w + W r, (2.3) One also has where ∆Tw = Tw – Tw 0 . The appearance of the constraint leads to an increase in the so-called supercoiling free energy. That energy, Gsc , depends quadratically on the linking number difference (with kB T as the energy unit): Gsc = (Ksc /N )(∆Lk)2 , (2.4) where Ksc is the supercoiling force constant [57]. A minicircle bearing a particle can be divided into two topologically distinct domains: the wrapped DNA, whose conformation is defined by histone interactions, and a free loop that is restricted only at its ends and adopts an equilibrium conformation elsewhere. In this case, the minicircle linking number difference becomes: ∆Lk = ∆Lkp +∆Lkl . (2.5) FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 255 This equation shows that ∆Lk p , the ∆Lk associated with the particle, is the ∆Lk of the topoisomer when the loop is relaxed (∆Lk l = 0). It is easy to see that ∆Lk is also equal to ∆Lk = ∆T wp +∆T wl +W r, (2.6) in which ∆Tw p and ∆Tw l are the twist changes on the histone surface and in the loop, respectively, and Wr the total writhe. Upon variations in ∆Lk, ∆Tw p remains constant but the other two terms change. When the loop is relaxed (∆Lk l = ∆Tw l = 0), Wr = Wr 0 , and Eqs. (2.5) and (2.6) combine into ∆Lk p = ∆T wp + W r0 . (2.7) The twist change in the particle is: ∆T wp = Np (1/hp − 1/h0 ), (2.8) where Np is the number of wrapped base pairs, and hp their intrinsic helical periodicity. In general, this periodicity shall not coincide with the periodicity of the DNA contacts with the surface [58] (but see below), which will be referred to as the local periodicity hloc (the periodicity in a local frame). If the vector normal to the double helix axis coincides with the normal to the surface (as is the case for the nucleosome), the relation between the two periodicities is [59]: T wp = Np /hloc + Θp /2π, (2.9) where Θp is the total geometrical torsion of the double helix axis in the particle. Because DNA wraps into a superhelix, the Frenet formulae of differential geometry can be used to give 2πwp Θp = q 2 (2πr) + p2 (2.10) where w is the number of turns of the superhelix, p its pitch (p < 0 for a left-handed superhelix), and r its radius. Eqs (2.9) and (2.10) imply that the inequality hloc 6= hp is a direct consequence of a superhelix with a non-zero pitch. However, it was recently recognized that this pitch is mostly defined by base pair longitudinal slides between successive, almost straight, DNA stretches [60]. Slide is here opposed to shift, which is the base pair lateral displacement. Strikingly, reconstruction of the superhelix with all base pairs parameters, except a zero shift, had little consequence on its geometry. In contrast, zeroing the slide resulted in a flattened superhelix (3 Å pitch, against 30 Å for the real superhelix) [60]. As a result, hloc increases to nearly the level of hp . hloc ∼ hp does not impinge on nucleosome and chromatosome calculations, 256 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL which do not use hloc , although there is a small effect on the geometry of the right-handed tetrasome (see Section 2.1, below). The free energy of the particle-bearing minicircle is given by the same quadratic dependence as in Eq. (2.4), except that ∆Lk in this equation is replaced by ∆Lk l , giving: Gsc = (Ksc /Nl )(∆Lk − ∆Lk p )2 + Gp , (2.11) where Nl is the number of bp in the loop, and Gp describes the free energy of bending in the relaxed loop and additional contributions from the particle (various DNA distortions on the histone surface, histone-DNA and histonehistone interactions, etc.). The experimental approach (Fig. 2, top), described in [61–63], involves first, the reconstitution of the particle on a negatively supercoiled topoisomer, and second, its relaxation with topoisomerase I. The result is an equilibrium mixture of particles on adjacent topoisomers (the starting topoisomer is not supposed to be a member of the equilibrium), and this mixture is electrophoresed in a polyacrylamide gel (Fig. 2, bottom right). The relaxed material is cut out from the gel (brackets), and eluted naked DNAs are electrophoresed in a second gel (Fig. 2, bottom left) to identify the topoisomers and quantify their relative amounts in the distributions (Fig. 2, profiles). The DNA length was changed by 1–2 bp increments at a time in order to get a rather continuous spectrum of Lk and ∆Lk (see Eq. 2.2). This was accomplished for three unique DNA sequences derived from a fragment of plasmid pBR322, the 5S rDNA nucleosome positioning sequence [64], and a fragment of human α-satellite (centromeric) DNA. This resulted in three respective DNA minicircle series, the 351–366 bp pBR series [65], the 349–363 bp 5S series [66], and the 346–358 bp α-satellite series [67]. DNA most probable helical periodicities, h0 , were measured (together with Ksc ) through relaxation of two naked minicircles of selected sizes within the series [66, 67]. Results are presented as a plot of the relative amount of each topoisomer in the equilibria as a function of ∆Lk, for all DNA minicircle sizes of a series (see Figs 3b, 6a–c and 8, below). The usual multimodality of that plot reflects the possibility for the particle to exist in 2 or 3 discrete conformational states characterized by specific values of ∆Lk p , Gp and, in general, Ksc . According to Boltzmann law, the probability of a particle in state i on topoisomer ∆Lk is proportional to f (i, ∆Lk) = exp(−Gsc (i, ∆Lk)) (2.12) where Gsc (i, ∆Lk ) depends on ∆Lk p (i), Gp (i) and Ksc (i) through Eq. (2.11). Neglecting the ±2% variation in N between 346 and 366 bp, N can be replaced by its mean, which gives: FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA F (∆Lk) = P 257 f (i, ∆Lk) i 3 P P (2.13) f (i, ∆Lk + j) j=−3 i where F (∆Lk ) is the ordinate in the experimental topoisomer-relative amounts-versus-∆Lk plot. Eq. (2.13) was fitted to that plot to find the values of ∆Lk p and ∆G p (∆G p is measured by reference to one of the states). With two states, Ksc /Nl values in Eq. (2.11) can also be obtained from the fitting. With three states, however, the accuracy would decrease due to the larger number of parameters, and Ksc values were instead calculated using the explicit solutions to the equations of the equilibrium in the theory of the elastic rod model for DNA (referred to below as the “exact solutions theory” [68–70]). In this theory, the loop domain is treated as a segment with specified conditions at its end points where it contacts the protein surface. Because particles have a two-fold symmetry, tangent vectors to the end points are symmetrical to each other with respect to the dyad axis. The end conditions are then defined solely by the distance between these two end points and the relative orientation of these two vectors, both of which depend upon the geometry of the histone-bound DNA. This geometry can be approximated by an ideal superhelix of pitch p and radius r. The DNA segment is treated in the theory as an inextensible, homogeneous body whose behavior can be described by the rod theory of Kirchhoff. The solutions to the equations of the equilibrium lead to the most probable conformation of the loop, with or without self-contacts, which minimizes the elastic free energy for specified end-conditions (in particular the pair of superhelix parameters p and r), and the loop torsional constraint, ∆Tw l (see Eq. 2.6). Once such a conformation is found, the elastic energy of the loop and the writhing of the whole minicircle can be calculated knowing the geometry of DNA in the particle (see [68] for details). The topoisomer ∆Lk can subsequently be calculated when the DNA twist in the particle, ∆Tw p , is specified (see Eq. 2.6). The elastic energy was found to vary with ∆Lk approximately according to a second-degree polynomial, which gives Ksc after identification with Gsc in Eq. (2.11) (neglecting thermal fluctuations, which is a reasonable approximation for a small loop). Applications of these experimental and theoretical tools to the different particles are presented in the following subsections. 2.1. The tetrasome chiral transition. Examples of tetrasomes reconstituted on ∆Lk = ±1 topoisomers of a 359 bp minicircle are shown in electron micrographs of Fig. 3a. In contrast to nucleosomes (Fig. 5, below), there is no hidden DNA turn wrapped around the histones, and the contour length of the particles is identical to that of the naked DNA (Fig. 3a). This is consistent with a horseshoe-shaped tetramer with ∼ 55 bp of DNA wrapped in ∼ 3/4 turn of a superhelix, as derived from the nucleosome crystal structure in Fig. 1b. Tetrasomes reconstituted on a short 258 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 2. The minicircle approach and its illustration for nucleosomes on pBR 356 bp DNA minicircle. Top scheme: Mainsteps involve: 1) reconstitution; 2) relaxation with a topoisomerase; 3) gel electrophoreis of chromatin products; and 4) extraction of DNA products and their gel electrophoresis (from Fig. 4 in [67]). Bottom: Reconstitutions were performed on a 32 P-labeled topoisomer of ∆Lk = −2.9 (see Eq. (2.2)) with control or acetylated (Acetyl.) core histones. Samples were incubated at 37 ◦C in relaxation buffer, either Tris (T: 50 mM Tris-HCL) (pH 7.5), 0.1 mM EDTA, 50 mM KCL, 5 mM MgCL2 and 0.5 mM dithiohreitol) or phosphate (P: same as Tris buffer with 50 mM potassium phosphate (pH 7.5) instead of 50 mM Tris-HCL), with (Topo I+) or without topoisomerase I (Topo I−). Electrophoreses were in polyacrylamide gels at room temperature. OC: open (nicked) circular DNA. TE: starting chromatin in TE buffer (10 mM Tris-HCL (pH 7.5), 1 mM EDTA]. Note the two bands in nucleosome relaxation products (NUC), and the shift in their stoichiometry from the first conditions to the second. Eluted DNA products (brackets) were electrophoresed in a chloroquine-containing polyacrylamide gel, together with control topoisomers (C1–C4). Radioactivity profiles allow quantification of the topoisomers. The gel autoradiographs are shown (from Fig. 4 in [129]). FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 259 Fig. 3. Tetrasomes visualized on ∆Lk = ±1 topoisomers, and their relaxation data on pBR DNA minicircle series. a) Panels 1–4: electron micrographs of tetrasomes on 5S 359 bp DNA minicircle. Panels 5: naked topoisomers (from Figs. 10a and 10b in [71]). b) Relaxation data acquired as shown in the scheme of Fig. 2 are shown as topoisomer relative amounts versus ∆Lk (∆Lk uses Eq. (2.2) with h0 = 10.494 (±0.003) bp/turn in Tris buffer; see legend to Fig. 2). The smooth curve was obtained from the fitted two-state model [Eqs. (2.11)–(2.13)] (from Fig. 5a in [73]). Relaxed left- and right-handed tetrasome DNA conformations were calculated using the exact solutions theory (from Fig. 3 in [80]). DNA fragment [71] or tandem repeats of 5S DNA [72] had a similar, although often uncrossed, hair-pin-like appearance. Results from relaxations of tetrasomes on the pBR minicircle series are shown in Fig. 3b. According to Eqs (2.11) and (2.13), a maximum in topoisomer probability should be observed when the minicircle ∆Lk coincides with ∆Lk p , i.e. when the loop is relaxed. It follows from this that the bimodal profile in Fig. 3b should reflect tetrasome access to two alternative DNA conformations, around ∆Lk = ∆Lk p = −0.7 and +0.6, respectively. Fitting the plot in Fig. 3b to a two-state model produces the linking number difference, ∆Lk p , of each state, their free energy difference, ∆G p , and their associated supercoiling force constant, Ksc [73]. ∆Lk p values, −0.74 and +0.51 for left- and right-handed states, approximately corre- 260 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL spond to the center of the peaks in Fig. 3b, as expected. The right-handed state is energetically unfavorable by 1.9 kB T relative to the left-handed state. Ksc values, 2400 and 1300 for the left- and right-handed states respectively, are quite different and both much lower than the naked minicircle value (4000). The naked DNA value was obtained around the relaxation point, i.e. when a change in the minicircle topological constraint should be stored almost entirely as torsion. It has been shown both theoretically [70, 74–76] and experimentally [77–79], that a threshold constraint is required before the onset of writhing in a minicircle, on the way to a figure-eight conformation. Here the loop is beyond the onset of writhing, and the low Ksc value simply reflects the fact that changing the writhe is easier in terms of energy than changing the twist by the same amount. However, an initial writhing of high energetic cost is required, and this energy is provided by histone-DNA interactions upon DNA wrapping. Interestingly, therefore, packing of DNA into a particle leads to a large increase in DNA conformational flexibility by overcoming this initial energetic barrier. Considering the existence of two states, the overall DNA flexibility is even larger. The exact solutions theory explains why the loop can be more flexible in the right-handed state than in the left-handed state (see their Ksc values above), or, more precisely, why a given topological constraint should change the writhe of the loop more, and its twist less, in the right- versus the lefthanded state. The reason is that the loop end-conditions change from one state to the other. Our reconstructions in Fig. 3b have a DNA superhelix radius of 5.1 nm in the right-handed state versus 4.7 nm in the left-handed state (against 4.3 nm in the nucleosome crystal structure). Such a lateral opening of right-handed particles was supported by electron microscopic visualization of a large number of tetrasomes on both linear and circular DNAs [71]. With hp = hloc (see above), the DNA helical periodicity on the tetrasome changes slightly, as well as the radius estimate in the right-handed state. One obtains hp = hloc = 10.3± 0.1 bp/turn and W r 0 = 0.43 ± 0.05, from hloc = 10.2± 0.1 bp/turn and W r0 = 0.31± 0.05 in [73, 80]. Such an h value, compared to 10.49 bp/turn for naked pBR DNA [63, 66], points to a significant DNA overtwisting in pBR tetrasomes. DNA is even more overtwisted on 5S tetrasomes, as indicated by hp = hloc = 10.2± 0.1 bp/turn, against 10.54 bp/turn for naked 5S DNA [80]. The 5S topoisomer amountsversus-∆Lk profile (not shown) is similar to that in Fig. 3b. A shift along the ∆Lk axis is observed, however, as a consequence of the larger overtwisting, resulting in ∆Lkp = −0.68 and +0.60 for left- and right-handed states. Moreover, the relative area of the “positive” peak is reduced compared to the pBR profile, reflecting a ∼ 50% higher transition free energy, ∆G p . Trypsinized tetramers, with H3, H4, or both H3 and H4 tails removed, where also studied [73]. Tail removal (especially H3’s) decreases the proportion of negatively supercoiled topoisomers in the relaxation equilibria, indicating a facilitation of the tetrasome chiral transition. A similar trend FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 261 was observed with tetrasomes reconstituted with moderately acetylated tetramers [73], but hyperacetylation turned out to be just as efficient in facilitating the transition as tail removal [81]. Trypsinized tetrasomes showed considerable changes in all parameters of the two conformational states. The transition free energy decreased by two-thirds, and a 10% lateral opening occurred in the left-handed conformation. These results reflect a regulatory role for the tails in the chiral transition. A hint at the mechanism of this regulation can be found in the nucleosome crystal structure, which shows the histone fold-proximal domain of the H3 tails passing through channels provided by the aligned minor grooves of the two gyres at superhelix locations SHL+7 and −1 and SHL−7 and +1 [1]. In the absence of the second gyre, these interactions may still occur at SHL±1. At such locations, H3 tail proximal domains may act as wedges against the narrowing of the minor groove, i.e. the local straightening of the DNA, resulting from the transition-associated opening. Then only upon their release could the tetrasome open and the transition to the right-handed conformation occur [73]. The spontaneous occurrence of the transition under physiological conditions, i.e. the lateral opening, suggests that the tails are transiently released (or destabilized) due to thermal motions. Such a release can only become more frequent upon a decrease in the tail/DNA interactions resulting from acetylation. The occurrence of a transition was initially proposed on the basis of tetrasome ability to assemble with similar efficiencies on both negatively and positively supercoiled DNA minicircles [82]. Negative and positive tetrasomes also had a similar appearance under electron microscopy, with a less-than-a-turn wrapping and crossed entry-exit DNAs (Fig. 3a). From this, the transition was thought to involve a change in chirality of the wrapped DNA, accompanied by a 360◦ rotation of the loop around the particle dyad axis and by a reversion of the crossing polarity from negative to positive. A reorientation of the two H3-H4 dimers in the H3/H3 four-helix bundle interface (Fig. 1b) was further suggested to mediate the change in the wrapping chirality. The involvement of the protein was directly demonstrated by the observation that a steric hindrance at the H3/H3 interface interferes with the transition. Bulky adducts introduced through thiol oxidation of H3 cysteines 110 (located on the interface) indeed oppose the transition or, on the contrary, block the tetramer right-handed [71, 82, 83]. This is the case of 5,5’-dithio-bis(2-nitrobenzoic acid) (DTNB), which was recently found to break the tetramer into its H3-H4 dimers [84]. This indicates that the stable positive supercoiling provided by DTNB-modified histones is acquired through a destabilized H3/H3 interface which reestablishes upon binding to DNA [84]. Similar results were obtained with the archeal histone-like HMf through mutagenesis at the HMf/HMf interface [85]. However, all our results with unmodified tetramers amply demonstrate that their chiral transition is smooth and does not require breaking them into dimers. 262 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL The proposed tetrasome chiral transition later received further experimental and theoretical support: i) ethidium bromide was found to hamper the transition, suggesting that the local base pair undertwisting resulting from its intercalation opposes DNA overtwisting in the dyad region that normally accompanies H3-H4 dimer reorientation [79]; ii) the neutron scattering pattern of tailless octamers exactly matches that predicted from the crystal structure, but the pattern of tailless tetramers does not [86], possibly as a reflection of the tetramer in solution being a mixture of left- and right-handed conformations [87]; iii) torsion of single tetrasome fibers in low salt revealed a centre of rotation similar to that of naked DNA (Fig. 13b, below), indicating that tetrasomes equilibrate equally between their two chiral forms; and iv) a molecular dynamics study (Normal Mode analysis) of the tetrasome revealed three lowest-frequency, i.e. most cooperative, vibrational modes, corresponding to movements of the whole H3-H4 dimers about each other (Fig. 4) [87]. The second of these modes involves dimer reorientation around an axis going through the two cysteines 110, while the third mode describes a lateral opening around an axis orthogonal to the former axis and intersecting it. These results explain our initial observation that the transition can occur unabated after cross-linking of these two cysteines through disulfide bridge formation [82]. 2.2. Nucleosome conformational flexibility. Monte-Carlo calculations [59], and later the exact solutions theory [68], showed that a canonical ∼ 1.7-turn nucleosome on a DNA minicircle with a relaxed loop has a writhe W r 0 ∼ −1.7, while a ∼ 1.4-turn uncrossed nucleosome has W r 0 ∼ −1.0. Such nucleosomes were visualized by electron microscopy on ∆Lk = −1 and −2 topoisomers of a pBR 359 bp fragment [88]. Interestingly, nucleosomes on the latter topoisomer fluctuate about equally between closed negative and open conformations in low salt (TE: 10 mM Tris-HCl and 1 mM EDTA, pH 7.5) (Fig. 5a), with the closed negative conformation being stabilized upon addition of 100 mM NaCl [88]. In contrast, nucleosomes on the ∆Lk = −1 topoisomer were frozen in the open conformation regardless of the salt concentration [88]. Moreover, most of nucleosomes on the ∆Lk = 0 topoisomer also had a crossed appearance [88], although their crossing must have been positive in order to compensate for the negative crossing inside the particle and minimize overtwisting of loop DNA. Nucleosome relaxation and subsequent gel electrophoretic fractionation of nucleoprotein and DNA products is illustrated in Fig. 2, bottom, for the particular example of 356 bp pBR minicircle. The resulting topoisomer relative amounts-versus-∆Lk plot of these nucleosomes (Fig. 6a) shows shoulders or peaks centered at ∆Lk values around −1.7, −1 and −0.5, which reflect nucleosome access to three distinct DNA conformations [63, 66]. As for tetrasomes, these peaks or shoulders must result from the relative energy benefit of relaxing into these particular topoisomers of ∆Lk FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 263 Fig. 4. Normal mode analysis of the tetrasome. a) The axes (thin red arrows) of the rotation components of the three main vibrational modes are shown for each mode, superimposed on the tetrasome DNA superhelix viewed along the dyad (blue dots and thick blue arrows) or the superhelical axis. The axis of mode 1 runs close to the dyad, and the axis of mode 3 is approximately parallel to the superhelical axis. Mode 2 axis is approximately perpendicular to both dyad and superhelical axes. All three axes traverse cysteines 110 (green balls). b) The tetrasome was perturbed along the direction of mode 2 toward a positive superhelical pitch (right) and allowed to relax without constraint until its energy reached a local minimum. The resulting tetrasome DNA superhelix (red; note its right-handedness) is shown superimposed onto the background side of the nucleosomal superhelix (green) viewed perpendicular to both dyad and superhelical axes. In contrast, a perturbation along the same mode toward a more negative pitch (left) does not lead to a local energy minimum, and the tetrasome returns to its initial conformation (yellow) (the figure is Fig. 4 in [87]). = ∆Lk p , because only these topoisomers can provide a relaxed loop to the nucleosomes in these particular conformations. The ∆Lk ∼ −0.5 figure readily suggests that the crossing in the closed positive conformation is not complete, and stops about half-way (see below). Application of the exact solutions theory to 1.45- and 1.7-turn nucleosomes led to Ksc /Nl estimates of 12 (±1) (Ksc ∼ 2500), only slightly different between the states [66]. Eqs (2.11–2.13) were fitted to the topoisomer relative amounts-versus-∆Lk plot in Fig. 6a, resulting in ∆Lk p (i) and ∆G p (i) values listed in Table 1 (+Mg2+ ). The closed negative state is the most favorable, and the closed positive state the least, as expected, while the open state, taken as a reference of energy, is intermediate. 264 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 5. Nucleosomes visualized on ∆Lk = −2 topoisomer, and model. a) Electron micrograph of chromatin on pBR 359 bp DNA minicircle in TE buffer. Gallery: a, naked topoisomer; b, open conformation; c, closed negative conformation (from Fig. 5 in [88]). b) Relaxed open, closed negative and positive 359 bp DNA conformations calculated using the exact solutions theory, with wrappings of 1.7 and 1.45 turns in closed and open states. Corresponding Wr values are −1.65 , −1.0, and −0.3 (from Fig. 4 in [80]). ∆G p (i) can be used to calculate the relative steady-state occupancy of state i, fi , by a nucleosome with a nicked loop, i.e. free from torsional constraint. Using the equation exp(−∆Gip ) fi = P exp(−∆Gip ) i (2.14) FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 265 Table 1 Nucleosome conformational state parameters on the three DNA series. ±M g 2+ refers to the presence or absence of MgCl2 in the relaxation buffer. hp was calculated in the open state. DNA (histones) Mg2+ + pBR (control) − pBR (acetylated, phosphate) + + 5S (control) − α-satellite (control) + α-satellite (CENP-A) State ∆Lkp ±0.02 ∆Gp (kB T ) ±0.1 negative open positive negative open positive negative open positive negative open positive negative open positive negative open positive negative open positive −1.69 −1.04 −0.56 −1.69 −1.04 −0.56 −1.73 −1.02 −0.61 −1.40 −0.72 −0.41 −1.40 −0.72 −0.41 −1.55 −0.79 −0.47 −1.55 −0.79 −0.47 −0.8 0 1.2 0.4 0 1.7 0.8 0 3.6 −1.7 0 ≥ 2.2 −0.6 0 ∞ −1.5 0 0.8 −0.1 0 2.7 h p (±0.03)/ h0 (±0.005) (bp/turn) 10.49/10.49 10.30/10.54 10.30/10.49 one obtains 63%, 28% and 9% of pBR nucleosomes in the closed negative, open and closed positive states, respectively. This provides a concrete picture of the energy dependence of the equilibrium. Interestingly, the above calculated Wr 0 is virtually identical to the fitted ∆Lk p for both closed negative and open states (Table 1). This coincidence reflects the absence of mean DNA overtwisting upon wrapping in pBR nucleosomes (∆Tw p = 0 in Eq. 2.7), which results in hp (the mean DNA helical periodicity on the histone surface; see Eq. 2.8) = hloc = h0 = 10.49 bp/turn (Table 1). This result, together with the above reported overtwisting on the tetramer surface, would suggest that the DNA wrapped on H2A-H2B dimers is undertwisted in the pBR nucleosome (see below). In contrast, 5S nucleosomes (Fig. 6c) show a ∼ 0.3 increase in ∆Lk p of both closed negative and open states, relative to Wr 0 values (Table 1; +Mg2+ ). This reflected a ∆Tw p ∼ 0.3 overtwisting relative to the naked DNA (hp = 10.30 bp/turn; Table 1), and a ∼ 0.2 overtwisting, i.e. ∼ 2 bp, relative to 266 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 6. Relaxation data of nucleosomes on pBR and 5S DNA minicircle series, and their alternative DNA positions. a)–c) Data were acquired as shown in Fig. 2, bottom, using h0 = 10.475 (±0.003) bp/turn for pBR DNA in phosphate buffer (see legend to Fig. 3b for h0 in Tris buffer), and h0 = 10.538 (±0.006) bp/turn for 5S DNA in Tris buffer. Smooth curves were obtained from the fitted three-state model (the figure is Fig. 5 in [129]). d) Electrophoretic fractionation in polyacrylamide gels of mononucleosomes on 357 bp 5S and 350 bp α-satellite DNA fragments. A subset of 5S nucleosome positions is marked (see their complete map in [21]). The diagram schematizes nucleosome position-dependent migration [53, 91] (from Fig. 2 in [67]). pBR nucleosomes (taking into account the h0 difference, in the opposite direction, between the naked DNAs; Table 1). Consistent with this discrepancy, a comparison of DNase I footprints of the two nucleosomes trimmed to core particles revealed the same local periodicity everywhere except for a ∼ 1 bp untwisting of pBR DNA relative to 5S DNA at each of the two dyad-distal sites (SHL±5) where H2B N-terminal tails pass between the FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 267 two gyres (Fig. 1a) [66]. α-satellite nucleosomes also show an overtwisting (∆Tw p ∼ 0.2) relative to naked DNA (Table 1) [67]. 5S nucleosomes access the negative state more frequently than do pBR nucleosomes (83% against 63% in the steady state equilibrium, respectively, calculated from Eq. (2.14) with corresponding ∆G p values in Table 1), but about the same as do α-satellite nucleosomes (76%). Their unique feature, however, is to hardly access the positive state (≤ 2%), in contrast to the other two (9% and 8%, respectively). Interestingly, this behavior is predicted by the loop elastic energy, Gsc , plotted as a function of ∆Lk in Fig. 7a (straight). The theoretical ∆Gsc ∼ 6kB T between positive and negative states is indeed similar to the 5S ∆(∆G p ) ≥ 4 kB T (Table 1). A closer look at the curve in Fig. 7a shows that the energy minimum of the negative state is located at the expected ∆Lk = −1.7 (in the absence of overtwisting), whereas the positive state minimum, at ∆Lk ∼ −0.3 (against ∆Lk p ∼ −0.6 for pBR nucleosome in Table 1), is not. This discrepancy may originate from the unfavorable position of the DNA self-contact in the loop (circles in Fig. 7a; straight), which prevents the true positive minimum to be reached, whereas the self-contact is too far on the left side of the curve to interfere with the negative state. Theoretical conformations for the three states are displayed in Fig. 5b [66]. With ∆Tw l = 0 at or around the Gsc minima in Fig. 7a, the twist contribution is cancelled and the entire loop elastic energy is in bending. It should be noted that there are other contributions to Gp in Eq. (2.11). Two of them originate from the DNA and favor the open state: an electrostatic repulsion between entry/exit DNAs, which is lower in the open state; and the straightening of the unwrapped DNA at the edges upon breaking of the contacts at SHL±6.5 (Fig. 1). Another contribution originates from the protein through these contacts, which stabilize both closed states (see below). The bending energy (∆G sc ) and the electrostatic repulsion can then be considered as the sole contributors to Gp . Due to the early DNA self-contact described above, electrostatic repulsion should contribute more to the energy of the positive state, and ∆G sc ∼ 6 kB T in Fig. 7a should be considered as a lower bound for the free energy difference between the two states. So why are the corresponding ∆(∆G p ) differences of pBR and αsatellite nucleosomes (∼ 2 kB T ; Table 1) much smaller than the predicted value, allowing their easy access to the positive state? A simple answer to this question is to suppose that the relative orientation of entry/exit DNAs can vary. If they are slightly less divergent than expected from the standard superhelix, the positive crossing would indeed become easier and the negative crossing more difficult, as observed. To quantify the effect, we curved the superhelix axis in order to bring the two DNA gyres in contact at the entry-exit points (Fig. 7b). As shown in the profile (Fig. 7a; curved), the difference in the state energies, 2 kB T , is now close to that of pBR and α-satellite nucleosomes. This curvature, called gaping, has subsequently 268 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 7. Loop elastic energy for two models of the nucleosome. a) The loop elastic energy, Gsc , was calculated as a function of the topoisomer ∆Lk using the exact solutions theory for 1.7 turn DNA superhelices (∆T wp = 0) with straight or curved axes, as indicated in b). Gsc minima at ∆Lk ∼ −1.7 and −0.3 correspond to closed negative and positive states. Starting from the midregion of the energy profiles, the points at which a DNA self-contact first occurs in the loop are indicated by empty circles. A similar energy profile (straight) had previoulsy been reported in [69] (from Fig. 6 in [66]). been explored as a possibility to improve nucleosome-stacking properties of the 30 nm chromatin fiber [89] and condensation of mitotic chromosomes [90]. The process requires a rotation of the two H3-H4 dimers around their H3/H3 interface in a clockwise direction that increases the pitch of the negative superhelix (Fig. 4b). This not only incurs at high energetic cost (∼ 20 kB T ; [89]), but is not supported by Normal Mode analysis of tetrasome structural dynamics (Fig. 4b, left). For these reasons, reorientation of entry/exit DNAs in pBR nucleosomes has probably little to do with gaping, but is more likely a consequence of the 1 bp undertwistings at SHL±5 where H2B tails pass in between the two gyres (see above and Fig. 1) [66]. Other reorientation mechanisms may exist, however, as suggested by the similar ability of α-satellite nucleosomes FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 269 to cross positively in the likely absence of undertwistings at SHL±5 (αsatellite nucleosomes resemble 5S nucleosomes with respect to mean twist; Table 1). At this point, it is important to remember that single pBR, 5S and α-satellite nucleosomes occupy multiple alternative positions (∼15 for 5S and pBR and ∼6 for α-satellite DNAs), as illustrated in Fig. 6d on linearized 5S and α-satellite minicircles. [Note that the fractionation in the gel is due to DNA curvature by the histones, which affects the molecule overall dimensions differentially, depending on the nucleosome position relative to the fragment ends [53, 91], exactly as was first observed with curved DNA [92].] These alternative nucleosomes are different from each other in a number of criteria, including their hloc [91], and the features investigated here are, therefore, averaged over those populations. In particular, if a relation exists between entry-exit DNA reorientation and undertwistings in pBR nucleosomes, it is, therefore, on a statistical, but not a one-to-one basis. Nucleosome conformational dynamics depends, therefore, on the DNA sequence (see a recent confirmation of this sequence-dependent nucleosome polymorphism in [50]), but also on the histone modification state. Relaxation of pBR nucleosomes reconstituted with acetylated histones in the presence of phosphate (Buffer P in Fig. 2, bottom) substantially modifies the relative amounts-versus-∆Lk profile (Fig. 6b) and led to large increases in ∆G p of both closed states, making the open state energetically more favorable (Table 1). The role of acetylation in favoring nucleosome opening is in keeping with H3 N-terminal tails interacting with entry/exit DNAs, as shown by UV laser-induced cross-linking of long mononucleosomes [93]. The tails contain most of the acetylatable lysine residues, and their acetylation decreases the tail’s overall positive charge. This in turn weakens the tails’ interactions with entry/exit DNAs, especially in the presence of phosphate [94], and the DNA mutual repulsion increases. Interestingly, a similar effect was obtained upon removal of MgCl2 from the relaxation buffer (Table 1; −Mg2+ ) (and addition of monovalent cations (K+ ) to keep ho constant; [66]). Mg2+ may stabilize tail interactions with entry-exit DNAs, or directly favor the closed states by cross-linking the DNAs at their points of contacts. The effects of acetylation and of mono- and divalent salts were recently analyzed in details using FRET to measure the distance of DNA ends of mononucleosomes reconstituted on short fragments [95]. Steady-state occupancies of closed negative and open states by acetylated nucleosomes in phosphate become 32% and 65% (as compared to the reverse figures, 63% and 28%, for control nucleosomes; see above) and only 3% (against 9%) for the closed positive state. Some histone variants favor nucleosome opening, such as H2A.Bbd, an H2A alternative enriched in transcriptionally active chromatin [96]. This was initially observed through micrococcal nuclease cleavage and FRET [97], and more recently by cryoelectron and atomic force microscopies [98]. This is also the case of CENP-A, an H3 variant of centromeric nucleosomes [99, 100], although its effect is somewhat subtler. The main changes in 270 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL the CENP-A histone fold domain are a 2-residue expansion in loop L1 (between helices α1 and α2; [1]) and a replacement of arginine residues at H3 equivalent positions 49 and 83 by a lysine and an asparagine, respectively. While the effect of the 2-residue expansion is not clear, the consequence of the replacements is straightforward. H3 arginines 49 (in the αN extension) and 83 (in L1) stabilize the DNA superhelix at entry/exit positions of the nucleosome and the tetrasome, respectively, through intercalation of their lateral chain into the small groove at SHL6.5 and 2.5 [1], which lysine and asparagine will not do. A destabilization at the entry-exit was indeed observed in CENP-A nucleosomes (where H3 was substituted for CENP-A), as the energy of both negative and positive states was increased by 1.5–2 kB T (Table 1). This further indicates that αN-DNA binding sites at SHL±6.5 are similarly effective in both conformations. The state occupancy can again be calculated using Eq. (2.14), and in turn the mean dynamic wrapping from wrappings in closed and open states (147 and 126 bp, respectively). When compared to H3 nucleosomes, CENP-A nucleosomes showed a 7(±2) bp steady state unwrapping, which is sufficient to compromise the binding of a linker histone and to promote dissociation of H2A-H2B dimers by nucleosome assembly protein 1 (NAP-1) [67]. NAP-1 is ineffective to remove tetramers, and it was replaced by heparin, a strong acidic polyelectrolyte. The (CENP-A-H4)2 tetramer was found much easier to release than the (H3-H4)2 tetramer, consistent with replacement at position 83. Such a preferential two-stage disassembly of CENP-A nucleosomes relative to conventional nucleosomes was proposed to promote their observed progressive clearance from the chromosome arms by proteolysis following CENP-A transient over-expression [101, 102]. If applicable to CENP-A normal expression, this mechanism may be relevant to the problem of CENP-A exclusive centromeric localization (reviewed in [103]). 2.3. Chromatosome enhanced conformational flexibility. Relaxations of H5-containing pBR and 5S nucleosomes in the absence of Mg2+ (Mg2+ caused their precipitation) resulted in bi-modal plots with two wellseparated peaks for negative and positive states, and no peak for the open state (Fig. 8, bottom). Fitting of the plots with the two-state model led to the values listed in Table 2. The two peaks are still observed with H5 globular domain (GH5 lacks both N- and C-terminal tails), although the positive peak is now substantially reduced in the 5S plot compared to the pBR plot (Fig. 8, top). Moreover, the peaks now partially overlap due to the smaller difference between their ∆Lk p values (∼ 1, against ∼ 1.5 with H5; Table 2). Such a rescue by GH5 of the positive crossing in 5S nucleosomes presumably results from a normalization, albeit incomplete, of the relative orientation of entry-exit DNAs following GH5-induced increase in wrapping (compare linear −H5 and +GH5 nucleosomes in the gallery of Fig. 9, top). Surprisingly, GH5 generally decreases the amplitude of the crossings relative to control nucleosomes, as reflected by a mean shift of FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 271 ∼ +0.2 in ∆Lk p (except for the positive crossing of 5S nucleosome, the ∆Lk p of which is instead shifted by ∼ −0.1; Tables 1 and 2). The opposite is observed upon addition of the tails, i.e. the whole H5 amplifies the crossings relative to the controls (mean ∆Lk p shift of −0.25 ). H5 also increases the loop flexibility in both states, as indicated by the low Ksc /Nl values, 4–6 (Table 2), against 12 in control nucleosomes (see above). Relaxation experiments conducted with engineered H5 tail-deletion mutants [104] made it clear that the N-terminal tail plays a negligible role in the observed features, and that they are entirely due to the long, highly positively charged, C-terminal tail. H5 C-terminal tail appears to act through the stem formed upon joining entry/exit DNAs together [21]. Mean stem lengths, measured on the molecules shown in Fig. 9 and others, were ∼ 10 bp in circular nucleosomes, and ∼ 30 bp in linear nucleosomes. With 10 bp, the contour length of the loop is 360 − 160 − 2 × 10 = 180 bp (360 bp is the minicircle size and 160 bp the length of wrapped DNA). The question then is how such a short loop can be that flexible. The exact solutions theory again gives the answer. Calculations showed that a 180 bp loop with its ends in contact reaches the observed mean value of Ksc /Nl = 4.5 only when the ends were parallel. In contrast, the rigidity increased rapidly upon introduction of an angle, or if the ends are moved apart from each other. The calculation further showed that the loop could not be significantly smaller than 180 bp, that is, the stem could not be significantly longer than 10 bp, if the large flexibility were to be preserved [104]. The occurrence of the stem also explains the extensive crossings observed. Indeed, the entry/exit duplexes are expected to be at an angle when they first come into close contact, so that they will tend to wind around each other along the stem to minimize bending. The winding will increase the loop net rotation angle around the dyad axis, shifting ∆Lk p of both states accordingly. Building on this structural information, a model of the H5-containing nucleosome was constructed, which provided a physical and mathematical continuity to the DNA from the histone surface to the loop. In the junction domain, nucleosome entry/exit DNAs come into contact under a chosen angle, and cross negatively or positively. A right-handed or lefthanded, respectively, double helix then insures the additional rotation of the loop around the dyad axis, and eventually brings the two duplexes into parallelism [104]. Fig. 9, bottom right, shows chromatosomes in the two states (with a relaxed loop). With small Ksc values, the loop rotates easily around the stem axis when submitted to a constraint (depending on the topoisomer ∆Lk ), keeping the supercoiling energy low. 3. The chromatin fiber. Nucleosome arrays were reconstituted on 2 × 18 tandem repeats of a 190 bp or 208 bp 5S nucleosome positioning sequence. They were subsequently ligated to one DNA spacer plus one DNA sticker at each end (Fig. 10a), and attached to the coated bottom of 272 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 8. Relaxation data of GH5-and H5-containing nucleosomes on pBR and 5S DNA minicircle series. Relaxations were in MgCl2 -deprived Tris buffer (see legend to Fig. 2), with increased KCl concentration to keep DNA helical periodicities unchanged (see text). Smooth curves were calculated using the fitted two-state model (from Figs. 2 and 3 in [104]). the flow cell of a “magnetic tweezers” set-up at one end and to a paramagnetic bead at the other end (Fig. 10b). The rotation of the magnets, and hence of the bead, exerts torsion on a chosen fiber. The fiber extension and the force exerted on it are measured from the recorded three-dimensional position of the bead [87, 105]. 3.1. Structural plasticity. Torsional behaviors are entirely described by the length-versus-rotation plots (Fig. 11) [106]. The response of the naked DNA (red in Fig. 11a) was obtained following chemical dissociation of the histones in situ. Its upper part corresponds to the elastic regime, and the quasi-linear compactions on both sides to the plectoneme regimes. The slope in these regimes is related to the radius and pitch of the plectoneme superhelical structures [106, 107]. The lower compaction on the negative side is due to force-dependent strand melting at high negative torsions, which relaxes the molecule. Compared to DNA, chromatin (blue in Fig. 11a) is shorter and its centre of rotation is shifted to negative values. These are the consequences of wrapping ∼ 50 nm of DNA, i.e. 150 bp, per nucleosome in a left-handed superhelix of ∆Lk p ∼ −0.8 ± 0.1 FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 273 Fig. 9. GH5/H5-containing nucleosomes visualized on linear and circular DNAs, and model. Electron micrographs of nucleosomes on 5S 256 bp DNA (−H5 and +GH5), 5S 357 bp DNA (+H5) (top), or ∆Lk = −1 topoisomer of pBR 359 bp minicircle (±H5). Linear nucleosomes were in TE buffer plus 50mM NaCl and 5mM MgCl2 , and circular nucleosomes in TE or TE plus 50–100 mM NaCl (with the same results; from Fig. 3 in [129] for linear nucleosomes and Fig. 5 in [62] for circular nucleosomes). Linear nucleosomes are schematized. H5-containing nucleosomes (with relaxed loops) were modeled using the exact solutions theory (W r = −1.89 and −0.39 in negative (lower) and positive (upper) states; from Fig. 8 in [104]). (see below). Further comparison of DNA and fiber profiles with respect to their breadth requires the two have the same maximal extension under the same force. Taking advantage of the invariance in length of the DNA rotational response [106], the DNA profile was renormalized by dividing all lengths and rotations by the ratio of the maximal lengths, and shifted in order for its center of rotation to coincide with that of the fiber (red crosses in Fig. 11b). Compared to DNA of the same length, therefore, the fiber 274 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Table 2 Conformational state parameters of H5- and GH5-containing nucleosomes. DNA series Linker histone H5 pBR GH5 H5 5S GH5 State negative positive negative positive negative positive negative positive ∆Lkp ±0.02 −1.89 −0.34 −1.57 −0.65 −1.76 −0.16 −1.26 −0.29 Ksc /Nl ±1 3 6 6 7 4 6 4 12 ∆Gp (kB T ) ±0.1 0 1.1 0 0.9 0 1.6 0 1.9 appears extremely flexible in torsion, i.e. it can absorb large amounts of torsion without much shortening. Consistently, the worm-like rope elasticity model [108, 109] gives a rotational persistence length of 5 nm, much smaller than the 80 nm of DNA (smooth black curves in Fig. 11b). Moreover, the fiber is also more flexible in bending, with a persistence length of 28 nm, against 53 nm for DNA. Except for the fiber rotational persistence length, obtained for the first time, all values are similar to those obtained by others [106, 110–112]. Interestingly, the fiber plectoneme regimes are less steep than those of DNA, with a slope of 25 nm/turn, against 90 nm/turn for DNA. A smaller pitch and radius of the fiber plectonemes would be expected from its smaller bending stiffness. Partial neutralization of DNA phosphates by the highly positively charged histone tails could also result in a closer DNA/DNA approach of the linkers, or of nucleosome-free gaps. This large torsional resilience of the fiber was interpreted as a reflection of nucleosome dynamic equilibrium between the three conformational states previously identified. A molecular model of the fiber architecture in the elastic regime was designed (Fig. 12), which quantitatively accounted for the upper part of the profile. The topological parameters derived from the model were actually close to those found above for 5S DNA (Table 1). The energy parameters showed an open state favored by ∼ 1 and ∼ 2 kB T over the negative and positive states, respectively [105], quite similar to the situation encountered with acetylated histones in phosphate (Table 1). The reason is the low salt buffer (TE is used to minimize artifacts of nucleosome attractive interactions [113]), which also enhances entry/exit DNA repulsion. Nucleosomes in the open state must then predominate in the relaxed fiber at, or close to, the center of rotation, while the equilibrium is displaced toward negatively or positively crossed nucleosomes upon application of negative or positive torsions. The plectonemic regime is entered after all (negative) or most (positive) nucleosomes are in the crossed conformations. FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 275 Fig. 10. Chromatin fibers and their micromanipulation with magnetic tweezers. a) Electron micrographs of typical fibers reconstituted on 2 × 18 tandem repeats of a 190 bp 5S DNA fragment before their attachment. Red arrowheads indicate the occasional presence of clusters of two or three close-packed nucleosomes devoid of linker DNA. Nucleosome-free DNA spacers and stickers (∼ 1100 pb total, ligated onto the fibers after reconstitution) flanking the arrays are well visible. b) Scheme of the fiber and the magnetic tweezers setup (the figure is Fig. 1 in [87]). 3.2. The nucleosome chiral transition. Provided that the torsion is not increased much beyond the zero-length limit on the positive side, forward and backward curves obtained upon increase or decrease of the torsion, respectively, more or less coincide (not shown). Beyond this limit, i.e. upon the application of typically +70 turns, the backward curve (green in Fig. 13a) departs from the forward curve (blue) on the positive side, revealing a hysteresis. The hysteresis was argued to reflect the trapping of positive turns in individual nucleosomes, through their transition to an altered form called reversome (for chirally-rever se nucleosome), rather than collective effects (e.g. chromatin loops stabilized by nucleosome/nucleosome attractive interactions) [87]. Shifts on the positive side were reproducible for any given fiber over many cycles of torsions/detorsions, and were directly proportional to the number of regularly-spaced nucleosomes it contained, with a rate of 1.3 ± 0.1 turns per such nucleosome [87]. [Close-packed nucleosomes in Fig. 10a appear rigid and do not participate in conformational [105] nor in chiral [87] dynamics.] With ∆Lk p ∼ −0.4 for positively crossed nucleosomes in the plectonemic regime [105], it comes for the reversome: ∆Lk p ∼ −0.4 + 1.3 ∼ +0.9. 276 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 11. Fiber and DNA torsional responses. a) Extension-versus-rotation curve under a force of 0.35 pN in TE buffer of a chromatin fiber reconstituted on 2 × 18 tandem repeats of a 5S 208 bp DNA fragment (blue) and its corresponding naked DNA after complete nucleosome dissociation in the presence of 100 µg/mL heparin (red). b) Extension-versus-rotation curve of another chromatin fiber and of its corresponding DNA after renormalization. Smooth curves were obtained using the worm-like rope model (see text), assuming an elastic response in bending, stretching and twisting (from Fig. 2 in [105]). The hysteresis may then reflect the reversome metastability, due to a barrier in the energetic landscape between the two forms of the nucleosome. Consistently, when a fiber in the backward curve was allowed to relax in real-time, at constant force and rotation, a time-dependent shortening was observed which reflected reversome return to the canonical state. The proportions of each state were calculated as a function of time and used to estimate the energy parameters of the transition. We obtained an equilibrium energy difference of ∼10 kB T relative to the ground state of the nucleosome (the open state) and an energy barrier of ∼ 30kB T [87]. The hysteresis depends on the presence of H2A-H2B dimers. After their depletion upon successive treatments with heparin and core particles (NCPs), the resulting tetrasome fiber showed (Fig. 13b, purple): (i) an extended structure of maximal length intermediate between those of the initial nucleosome fiber and naked DNA; (ii) no hysteresis upon return from high positive torsions; and (iii) a center of rotation approximating that of the naked DNA. The first feature is consistent with the smaller wrapping in tetrasomes relative to nucleosomes, the second with the strict dimer requirement of the hysteresis, and the third with tetrasomes ability to fluctuate between left- and right-handed conformations of nearly equal and opposite ∆Lk p (see Section 2.1). The requirement to break docking of dimers on the tetramer is expected to be a major contributor to the energy barrier. This view is in FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 277 Fig. 12. The fiber three-state molecular model. Top: diagrams of nucleosomes in negative, open and positive states. Bottom: the model, fitted to data of Fig. 11b, predicts the response over 30 turns around the apex (bold red curve). Beyond these torsions, the thin red straight line represent the best fit of a plectoneme model (not described). Under the curve are shown typical structures of the fiber at torsions marked by black circles (structures 1 at the apex, 2 and 3 at the thresholds on negative and positive plectonemic regimes). In structure 1, steady-state proportions of nucleosomes in open, positive and negative conformations are 65%, 20%, and 15%, respectively, in structures 2 and 3, 100% and 80% are negative and positive, respectively, the remaining 20% are in the open state (from Fig. 5 in [105]). keeping with an estimate of ∼ 17 kB T for the binding energy of each dimer onto the tetramer [114]. A mechanical (or elastic) barrier is also likely to exist beyond the point of dimers undocking: twist may accumulate at the expense of writhe and be suddenly released, generating an instability similar to that previously predicted for twisted rods [115]. The histoneimposed DNA curvature is expected to enhance the writhing instability, in conjunction with the extra lateral opening of the structure required at mid-transition to relieve the clash between entry/exit DNA arms [73]. The reversome ∆Lk p is close to that of the right-handed tetrasome (+0.9 against +0.6 for 5S tetrasomes; see Section 2.1). Based on the similarity between the torsional response of the tetrasome fiber (purple in Fig. 13b) and the backward curve of the nucleosome fiber (green) with respect to their breadth and center of rotation, we have proposed: 1) the 278 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL Fig. 13. The fiber hysteretic response. a) Forward (blue) and backward (green) extension-vs-rotation curves in TE buffer of a 2 × 18 5S 190 bp fiber under a force of 0.35 pN after excursion at high positive torsions. b) Torsional response of the same fiber in TE (purple) after successive treatments with 1 µg/mL heparin in TE buffer, and 1 µg/mL nucleosome core particles (NCPs) in TE buffer plus 50 mM NaCl, under a steady high positive torsion. Similar results were obtained when H2A-H2B dimers were removed instead with 700 mM NaCl or upon transient application of a force of 3.5 pN (not shown). Moreover, the evidence that no (H3-H4)2 tetramers were removed by the treatment was provided by the rescue of the initial fiber length and torsional behavior upon incubation with H2A-H2B dimers [87]. c) Corresponding naked DNA response after heparin-depletion of all histones and return to TE buffer (black) (from Fig. S1 in Supplemental Data to [87]). reverse, right- to left-handed, transition process to be common to both particles; and 2) the reversome core to be a right-handed tetrasome. The hysteresis observed for the nucleosome fiber, but not for the tetrasome fiber, may then solely reflect the H2A-H2B-linked energetic barrier in nucleosomes. In the first step of the transition, dimers are expected to break their docking on the tetramer (Fig. 14). In the second step, the tetramer may undergo the chiral transition. We know that the right-handed 5S tetrasome partitions its ∆Lk p = +0.6 into Wr = +0.4 and ∆Tw = +0.2 (see Section 2.1) [80]. Assuming a similar ∆Tw on the reversome (if H2A-H2B dimers do not contribute), one gets Wr = +0.7 (+0.9 − 0.2). This writhe is intermediate between that of the above tetrasome, +0.4, and that of a virtual right-handed nucleosome mirror image of the open-state nucleosome, +1. The reversome may then be substantially more open than the open nucleosome, although both particles fold a similar length of DNA (the similar maximal fiber extensions in forward and backward curves necessarily reflect similar length components along the direction of the force). As a consequence, dimers may not be strongly docked on the reverse tetramer, as expected from their less favorable new interface in reversomes (see arrows on H2As; Fig. 14). Moreover, H3 αN -extensions (and N-terminal tails) are no longer appropriately located to interact with, and stabilize, FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 279 Fig. 14. Scenario for the nucleosome-reversome transition. Individual H2As and H2Bs in nucleosome upper and lower faces are differentiated by light and dark colors and for H2A also by arrows. The two distal 10 bp DNAs are straight in step 2 as a result of the breaking of the H3 αN -entry-exit/DNA binding sites. Two alternative routes for refolding into the reversome are shown beyond step 4. In model I, entry-exit DNAs with bound H2A-H2B dimers tend to wind around each other. In model II, the DNAs plus the dimers tend to continue the tetrasome right-handed superhelix. The DNA diameter is not to scale to better show the histones (the figure is Fig. 7 in [87]). reversome entry-exit DNAs (Fig. 14). Two possible paths for those DNAs, which incorporate these features, are illustrated in Fig. 14. In model I, the dimer-bound DNA duplexes tend to wind around each other along the dyad axis. In model II, they instead try to continue the right-handed superhelix of the tetrasome, helped by the dimers that would somehow extend the tetramer’s positive superhelical spool. 4. New solutions to old problems. The intricacies of DNA topology in chromatin. Reconstitutions of minichromosomes on DNA plasmids showed that the number of nucleosomes assembled did not depend significantly on the plasmid supercoiling [116]. With nucleosomes believed at that time to have a unique closed negative conformation, it was instead expected that the positive torsional stress resulting from their formation would hinder further reconstitution when the plasmids were relaxed or slightly positively supercoiled. At the same time, a number of physicochemical criteria indicated that the positively constrained nucleosomes were structurally identical to regular nucleosomes, raising the question of how so much stress could be dissipated. Moreover, whichever hidden alteration had occurred to the particles, it was entirely reversible upon release of the con- 280 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL straint, as shown by topoisomerase I relaxing them into canonical particles of mean h∆Lkn i ∼ −1 [117–120] (see below). Nucleosome conformational dynamics provides a simple explanation to this enigma: the equilibrium shifts progressively to positively crossed nucleosomes upon reconstitution. Such almost topologically neutral nucleosomes (internal negative and external positive crossings compensate) lost much of their otherwise adverse influence on further nucleosome assembly. In another experiment, negative supercoiling was introduced in naked and reconstituted plasmids using DNA gyrase. The maximal DNA supercoiling density reached (σ = ∆Lk /Lk o (see Eq. 2.2) ∼ −0.1) was nearly identical before and after reconstitution (measured in this latter case after deproteinization) [121]. Again, subsequent treatment with topoisomerase I resulted in canonical h∆Lkn i ∼ −1 particles. Such a transparency of nucleosomes to DNA gyrase did not require DNA untwisting on the histone surface, as then hypothesized, but only a displacement of the equilibrium, now toward the negatively-crossed conformation, as quantitatively shown in [61]. The unit h∆Lkn i value itself reflects an old problem: the so-called linking number paradox, which emerged from the necessity to reconcile topological and structural data of nucleosomes and chromatin [122–124]. With DNA assumed to continue the 1.75-turn left-handed superhelix revealed by the first crystal structure of the core particle [125], nucleosomes were viewed as two-turn particles, and as such should have reduce Lk by two turns (one-turn per negative crossing) instead of one. The early-proposed solution to the paradox was contained in Eq. (2.3): a positive ∆Tw, i.e. a DNA overtwisting on the histone surface, if sufficiently large, can satisfy ∆Lk n = −1 [122, 126, 127]. Later on, this solution lost some of its luster when it was shown that the overtwisting observed was definitely too small [128]. Again, nucleosome conformational dynamics provides the explanation (reviewed in [129]): h∆Lkn i = −1 simply reflects the steady-state proportions of nucleosomes with negative and positive crossings. h∆Lkn i in the minicircle system can be calculated from the stateaveraged ∆Lk p pondered by the state occupancy (fi ; Eq. 2.14). It writes: X fi ∆Lkpi (4.1) h∆Lkp i = i where ∆Lk ip are taken in Tables 1 and 2. Table 3 shows that h∆Lk p i varies substantially from control to acetylated histones in phosphate, and from GH5 to H5. In contrast, it varies little between pBR and 5S nucleosomes (mean ∆h∆Lkp i = +0.07), despite a more than 3-fold larger difference in ∆Lk p of the individual states (mean ∆(∆Lk p ) = +0.25). h∆Lk p i is found equal to −1.15 for 5S nucleosomes in the absence of Mg2+ (Table 3), not much different from h∆Lkn i = −1.0 for 5S minichromosomes relaxed under similar conditions [118, 119]. Moreover, the shift of h∆Lk p i between control and acetylated histones in phosphate (+0.25 ), as well as FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 281 upon Mg2+ depletion (mean = +0.2 over 5S and pBR nucleosomes; Table 3), is identical to that observed with minichromosomes from control to hyperacetylated histones (−1.04 ± 0.08 to −0.82 ± 0.05; [119]). The center of rotation of fibers micro-manipulated in magnetic tweezers also shifts by the same amount (0.25 ± 0.05 turn per nucleosome) upon addition of 2 mM MgCl2 and 40 mM NaCl [105]. It can be concluded that increasing the repulsion of nucleosome entry/exit DNAs, whether in a minichromosome, a fiber or a minicircle, either through a decrease in ionic strength or upon histone acetylation, similarly displaces the equilibrium toward the open state. Table 3 h∆Lkp i (±0.05) calculated from Eq. (4.1). acetylated/ phosphate −1.25 control −Mg2+ −1.25 +GH5 +H5 pBR control +Mg2+ −1.4 −1.3 −1.5 5S −1.3 −1.25 −1.15 −1.15 −1.5 We now believe, in view of the apparent absence of a relation between nucleosome DNA overtwisting and ability (or inability) for positive crossing (cf. contrasting data of 5S and α-satellite nucleosomes; Table 1), and contrary to a previous statement in [129], that h∆Lk n i need not be an invariant, at least in vitro. h∆Lkn i = −1.0 was indeed obtained with 5S minichromosomes made of overtwisted nucleosomes of ∆Lkp = −0.7 in the open state (Table 1). In the absence of overtwisting and with ∆Lk p (open) = −1 (pBR in Table 1), the dominance of the negative state over the positive state should draw h∆Lk n i below −1.0. A deviation of h∆Lk n i of 10–20% from the unit value would hardly have been detected in reported experiments with SV40 or other non-5S minichromosomes [117, 130–132] in particular because the number of nucleosomes was not measured with sufficient precision. The influence of the linker histone on DNA topology in minichromosomes is also unclear. A series of measurements showed little effect of H1/H5 on h∆Lk n i [117, 120, 130, 133, 134], but other data [131, 135] rather pointed to a large effect. It is also interesting that h∆Lk n i was not shifted when hyperacetylated SV40 minichromosomes were assembled in vivo (and relaxed in vitro) [130]. These discrepancies suggest the existence of nucleosome interactions that interfere with the measurements by hindering their mutual rotation around the dyad axis, preventing the thermodynamic equilibrium to be reached. Similarly, minichromosomes show an abnormally low ability of their internucleosomal linker DNAs to untwist upon an elevation of their relaxation temperature (the so-called thermal flexibility) [133, 136], with the notable exceptions of yeast chromatin [137] and our single nucleosomes on DNA minicircles [65]. Nucleosome interactions would be expected to be negligible at low nucleosome density, and 282 ANDREI SIVOLOB, CHRISTOPHE LAVELLE, AND ARIEL PRUNELL maximal at the saturated density achieved in vivo, explaining the SV40 data above [130]. The effect was directly observed in an experiment involving the binding of H5 to minichromosomes containing a variable number of nucleosomes. H5 again had little influence on h∆Lk n i at high densities, but the shift at low densities was comparable to that observed with single nucleosomes in Table 3 [131]. 5. Physiological relevance and prospects. The unique features of nucleosome conformational dynamics and chiral transition in chromatin fibers and DNA minicircles strongly appeal to their physiological relevance. Chromatin torsional resilience, mediated by the nucleosome conformational dynamics, may serve to cushion the supercoiling waves generated by polymerases upon replication or transcription (positive downstream and negative upstream; [138, 139]), and may actually be for these mechanisms the oil drop within the gear [140]. That resilience should even increase in the presence of the linker histone, as suggested by the enhanced loop flexibility resulting from stem formation between entry-exit DNAs (Section 2.3 and Table 2). This holds even if H1 binding is dynamic rather than static, as shown by its high exchangeability in vitro and in vivo [141–145]. With a deficit of H1 in active chromatin, nucleosomes should tend to adopt the open conformation (see [146, 147] for recent reviews of H1 role in regulating chromatin function). Consistently, transcriptional activity is tightly associated with histone acetylation [148, 149], which also favors the open state (Section 2.2 and Table 1). The open state facilitates the release of H2AH2B dimers, as recently shown in vitro using NAP-1 (a histone chaperone) as a histone acceptor [67]. This further leads to additional unwrapping and to formation of single-turn tetrasomes [67], which expose more sites of potential binding to protein effectors. Reversomes may be the last recourse when positive supercoiling waves can no longer be absorbed by the fiber. The formal condition for this is met since RNA polymerases exert a torque > 1.25 kB T /rad, equivalent to an energy > 8 kB T over one turn [150], as compared to a transition free energy of ∼ 10 kB T /turn in TE (Section 3.2) and ∼ 6 kB T /turn in 50 mM salt [87]. The chiral transition may not, however, be a safeguard only, but may also be mechanically linked to transcription in vivo. We have proposed that the chiral-switching ability of the tetramer is used by the main polymerase to break docking of H2A-H2B dimers [87]. This idea is supported by the observation that a single nucleosome on a short DNA fragment, in which torsional constraints cannot develop due to free rotation of the ends, presents an almost absolute block to in vitro transcription by RNA polymerase II at physiological ionic strength [7]. The block is relieved in higher salt (> 300 mM KCl), i.e. under conditions favoring dimer loss, and enzymes such as ACF or elongation factors such as FACT, which promote removal of a dimer, facilitate transcription elongation [151, 152]. Thus, dimers are likely to introduce a strong barrier to transcrip- FLEXIBILITY OF NUCLEOSOMES ON CONSTRAINED DNA 283 tion also in vivo, and the tetramer chiral flexibility may, via the dynamic supercoiling, concur with local endogenous activities to destabilize them. Once reversomes are formed at a distance, they should be easily transcribed owing to their open structure and destabilized dimers (Section 3.2). Such reversomes may be viewed as transiently activated nucleosomes poised for polymerase passage. Endogenous relaxing activities are not expected to interfere significantly with the above processes. Topoisomerase II (topo II) is notable since it was shown in yeast to relax chromatin five times as fast as topo I (topo I relaxes naked DNA twice as fast as topo II under the same conditions) [153]. The transcription-generated supercoiling was recently measured in B-cells using an activatable site-specific recombinase to excise a chromatin fragment positioned between two divergent promoters of a reporter gene (c-myc), which trapped the transient unrestrained negative supercoiling as chromatin circles. Before slowly decaying (in ∼ 30 min), that supercoiling was able to trigger non-B-DNA structure in a specific supercoiling-sensing sequence located within a linker six nucleosomes upstream of the promoters. This non-B-DNA structure in turn recruited two transcriptional factors essential for the expression of the gene [154]. 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