Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure

The regulation of chromatin biology ultimately depends on the manipulation of its smallest subunit, the nucleosome. The proteins that bind and operate on the nucleosome do so, while their substrate is part of a polymer embedded in the dense nuclear environment. Their molecular interactions must in some way be tuned to deal with this complexity. Due to the rapid increase in the number of high-resolution structures of nucleosome-protein complexes and the increasing understanding of the cellular chromatin structure, it is starting to become clearer how chromatin factors operate in this complex environment. In this review, we analyze the current literature on the interplay between nucleosome-protein interactions and higher-order chromatin structure. We examine in what way nucleosomes-protein interactions can affect and can be affected by chromatin organization at the oligonucleosomal level. In addition, we review the characteristics of nucleosome-protein interactions that can cause phase separation of chromatin. Throughout, we hope to illustrate the exciting challenges in characterizing nucleosome-protein interactions beyond the nucleosome.     

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin structure has played important roles during evolution.     

Ionic Strength and the Contraction Kinetics of Skinned Muscle Fibers

The influence of KCl concentration on the contraction kinetics of skinned frog muscle fibers at 5–7°C was studied at various calcium levels. The magnitude of the calcium-activated force decreased continuously as the KCl concentration of the bathing solution was increased from 0 to 280 mM. The shortening velocity at a given relative load was unaffected by the level of calcium activation at 140 mM KCl, as has been previously reported by Podolsky and Teichholz (1970. J. Physiol. [Lond.]. 211: 19), and was independent of ionic strength when the KCl concentration was increased from 140 to 280 mM. In contrast, the shortening velocity decreased as the KCl concentration was reduced below 140 mM; the decrease in velocity was enhanced when the fibers were only partially activated. In the low KCl range, the resting tension of the fibers increased after the first contraction cycle. The results suggest that in fibers activated at low ionic strength some of the cross bridges that are formed are abnormal in the sense that they retard shortening and persist in relaxing solution.     

Electric and Flow Linear Dichroism of Unfolded and Condensed Chromatin: A Comparative Study at Low and Intermediate Ionic Strength

Abstract

Identical samples containing polynucleosomal chains of chicken erythrocyte (CE) and Ehrlich ascites tumour (EA) chromatin were studied under various ionic conditions with regard to electric linear dichroism (ELD) and flow linear dichroism (FLD). Both orientation techniques consistently confirmed that, in the limit of very low ionic strength and in the absence of multivalent cations, the reduced linear dichroism of chromatin is negative in the DNA-base absorption band, as expected for an extended zig-zag polynucleosomal conformation. With increasing electrolyte content, both ELD and FLD decreased drastically in amplitude, but in contrast to the ELD which remains negative in an intermediate range of low ionic strength (0.1–0.5 mM Mg²⁺) the FLD changes sign and becomes positive. The ELD and FLD amplitudes decrease with higher Mg²⁺ concentrations and FLD even vanishes in the region of 0.2–0.4 mM; both signals are positive above 0.4–0.5 mM Mg²⁺.

The origin of the dissimilarities between ELD and FLD observations is still not fully understood. Several possibilities are considered: ELD signals are more influenced than FLD by the presence of short chromatin chains, nucleosomes and small pieces of naked DNA, while FLD is more susceptible to the presence of large, easily orientable, scattering aggregates. Different preferred orientation directions of the chromatin fibre with respect to electric and hydrodynamic fields may also be involved. Finally, FLD and ELD probably “see” different features of the chromatin structure.     

The Influence of pH and Ionic Strength on the Electrokinetic Stability of the Human Erythrocyte Membrane

The electrokinetic stability of washed normal human erythrocytes is discussed from the point of view of pH, ionic strength, and composition of the suspending medium. Many of the electrophoretic characteristics at low ionic strengths (sorbitol to maintain the tonicity), such as the isopotential points, are shown to arise principally from adsorption of hemolysate. The concept of electrokinetically stable, metastable, and unstable states for the red cell at various ionic strengths is introduced in preference to the general term "cell injury." In the stable state which exists around pH 7.4 for ionic strengths >0.007, no adsorption of hemolysate occurs, in the metastable state reversible adsorption of hemolysate occurs, and in the unstable state, in which ionic strengths and pH ranges are outside the metastable range, the membrane undergoes irreversible hemolysate adsorption or more general hydrolytic degradation. It is deduced from the equivalent binding of CNS, I, Cl, and F, the pH mobility relationships, and the conformation of the ionic strength data in the stable state to a Langmuir adsorption isotherm, that the membrane of the human erythrocyte behaves as a macropolyanion whose properties are modified by gegen ion association and in some instances by hemolysate adsorption. The experimental results are insufficient to establish conclusively the nature of the ionogenic groupings present in the membrane interphase.     

Tension in Skinned Frog Muscle Fibers in Solutions of Varying Ionic Strength and Neutral Salt Composition

The maximal calcium-activated isometric tension produced by a skinned frog single muscle fiber falls off as the ionic strength of the solution bathing this fiber is elevated declining to zero near 0.5 M as the ionic strength is varied using KCl. When other neutral salts are used, the tension always declines at high ionic strength, but there is some difference between the various neutral salts used. The anions and cations can be ordered in terms of their ability to inhibit the maximal calcium-activated tension. The order of increasing inhibition of tension (decreasing tension) at high ionic strength for anions is propionate^- SO₄^-- < Cl^- < Br^-. The order of increasing inhibition of calcium-activated tension for cations is K⁺ Na⁺ TMA⁺ < TEA⁺ < TPrA⁺ < TBuA⁺. The decline of maximal calcium-activated isometric tension with elevated salt concentration (ionic strength) can quantitatively explain the decline of isometric tetanic tension of a frog muscle fiber bathed in a hypertonic solution if one assumes that the internal ionic strength of a muscle fiber in normal Ringer's solution is 0.14–0.17 M. There is an increase in the base-line tension of a skinned muscle fiber bathed in a relaxing solution (no added calcium and 3 mM EGTA) of low ionic strength. This tension, which has no correlate in the intact fiber in hypotonic solutions, appears to be a noncalcium-activated tension and correlates more with a declining ionic strength than with small changes in [MgATP], [Mg], pH buffer, or [EGTA]. It is dependent upon the specific neutral salts used with cations being ordered in increasing inhibition of this noncalcium-activated tension (decreasing tension) as TPrA⁺ < TMA⁺ < K⁺ Na⁺. Measurements of potentials inside these skinned muscle fibers bathed in relaxing solutions produced occasional small positive values (<6 mV) which were not significantly different from zero.     

Effect of in vivo Histone Hyperacetylation on the State of Chromatin Fibers

Abstract

We evaluated the contribution of in vivo histone acetylation to the folding of chromatin into its higher-order structures. We have compared high-order folding patterns of hyperacetylat- ed vs. unmodified chromatin in living green monkey kidney cells (CV1 line) using intercalator chloroquine diphospate to induce alterations in the twist of internucleosomal linker DNA. We have shown that histone hyperacetylation induced by antibiotic Trichostatin A significantly alters intercalator-mediated chromatin folding pattern.     

A Model of Photon Cell Killing Based on the Spatio-Temporal Clustering of DNA Damage in Higher Order Chromatin Structures

We present a new approach to model dose rate effects on cell killing after photon radiation based on the spatio-temporal clustering of DNA double strand breaks (DSBs) within higher order chromatin structures of approximately 1–2 Mbp size, so called giant loops. The main concept of this approach consists of a distinction of two classes of lesions, isolated and clustered DSBs, characterized by the number of double strand breaks induced in a giant loop. We assume a low lethality and fast component of repair for isolated DSBs and a high lethality and slow component of repair for clustered DSBs. With appropriate rates, the temporal transition between the different lesion classes is expressed in terms of five differential equations. These allow formulating the dynamics involved in the competition of damage induction and repair for arbitrary dose rates and fractionation schemes. Final cell survival probabilities are computable with a cell line specific set of three parameters: The lethality for isolated DSBs, the lethality for clustered DSBs and the half-life time of isolated DSBs.By comparison with larger sets of published experimental data it is demonstrated that the model describes the cell line dependent response to treatments using either continuous irradiation at a constant dose rate or to split dose irradiation well. Furthermore, an analytic investigation of the formulation concerning single fraction treatments with constant dose rates in the limiting cases of extremely high or low dose rates is presented. The approach is consistent with the Linear-Quadratic model extended by the Lea-Catcheside factor up to the second moment in dose. Finally, it is shown that the model correctly predicts empirical findings about the dose rate dependence of incidence probabilities for deterministic radiation effects like pneumonitis and the bone marrow syndrome. These findings further support the general concepts on which the approach is based.     

Metal Sorption to Pseudomonas fluorescens: Influence of pH,Ionic Strength and Metal Concentrations

Migration behavior of radionuclides should be understood in order to estimate the impact of high-level radioactive waste (HLW) disposal on the environment. Bacteria, one of the major organic sorbents in solid and aquatic environments, can affect the fate of actinides and lanthanides by sorption onto their cell surfaces. In this study, the sorption of the radionuclide Americium (Am(III)) and several metal ions (Eu(III), Cu(II) and Ca(II)) to Pseudomonas fluorescens were measured under various conditions. It was revealed that as pH decreased, the sorption of Eu(III) and Am(III) increased when the metals were at relatively low concentrations but decreased at higher metal concentrations. On the other hand, sorption of Cu(II) followed the opposite trend. In the case of calcium, an increase in calcium ions was observed due to release from the cells. These findings suggest that the sorption mechanisms for low levels of Eu(III) and Am(III) on the cells of Pseudomonas fluorescens are different from those of Cu(II), Ca(II), and high concentrations of Eu(III) (> 10 ^{? 5} M).     

牛肾细胞染色体中染色质纤维的包装及RNP的分布

应用培养的牛肾（ＢＫ）细胞及分离的ＢＫ细胞染色体做常规透射电镜样品,经表面舒展技术和临界点干燥制备ＢＫ细胞染色体的扫描电镜样品,并结合电镜细胞化学研究了ＢＫ染色质纤维的包装及核糖核蛋白（ＲＮＰ）的分布。观察到ＢＫ染色体具有多级双股螺旋结构。在染色体横切面中,可见染色体中央有一低电子密度的无染色质区,该区内有大量ＲＮＰ物质。在染色质区ＲＮＰ较少,分布在染色质纤维间,与中央轴区的ＲＮＰ相连续,表明ＲＮＰ在染色体中呈不均匀分布。     

Partial Proteolytic Digestion of the Mammary Prolactin Receptor: Identification of Smaller Prolactin Binding Fragments

Abstract

Partial proteolytic digestion of the mammary prolactin (PRL) receptor was used to generate receptor fragments and analyze their immunoreactivity and PRL binding properties. Tryptic digestion of the PRL receptor produced two immunoreactive fragments (Mr ≈ 30,000 and ≈ 15,000) that reacted with a monoclonal anti-PRL receptor antibody and still specifically bound PRL, while the complete immunoreactive PRL binding unit (Mr ≈ 42,000) disappeared. Neither chymotrypsin nor V8 protease were able to generate any immunoreactive receptor fragments. These receptor fragments may represent smaller PRL binding receptor form(s) of biological significance.     

Effect of Ionic Strength on the Kinetics of Trypsin and Alpha Chymotrypsin

The kinetic effects resulting from changes in the medium ionic strength on reactions involving trypsin or α-chymotrypsin are different. The reaction rate increases continuously as the ionic strength increases with α-chymotrypsin. With trypsin, the rate increases at low ionic strengths but as the ionic strength further increases a gradual inhibitory effect is observed. The effects produced by different salts of various valence types (from uni-univalent to uni-trivalent or tri-univalent) are essentially the same, and they are a function of the square root of the ionic strength. The quantitative differences among the various salts may be accounted for on the basis of individual properties of the ions, such as the size of the hydrated ion, "association," etc. The effects of salts on the enzymic reactions described herein are amenable to the same electrostatic treatment applicable to non-enzymatic reactions. By applying Brönsted's basic kinetic concepts and the Debye-Hückel law of electrolyte activity, it appears that the salt effects are mainly due to changes in the dissociation of ionizable groups. This appears to be a general method for analyzing the effect of inorganic ions on enzymic reactions.     

Effect of Calcium on the Structure and Template Activity of Pea Chromatin

The absorption spectrum of native pea chromatin solubilizedunder minimal shearing conditions changed with increasing Ca²⁺concentration; the ratio of maximum to minimum absorption decreasedand the maximum absorption peak shifted to a longer wavelength.The concentration of Ca²⁺ to cause half complete sedimentationof chromatin was much lower for the solubilized native chromatin(more condensed and larger in size) than for the sonicated chromatin(less condensed and smaller in size). Solubilized native chromatinshowed a two-step melting profile in the absence of Ca²⁺. In the presence of Ca²⁺ the two T_ms disappeared and a new higherT_m appeared. Template activity of solubilized native chromatinincreased 3-fold upon dispersion and fragmentation by sonication.Addition of a small amount of ethylene glycol-bis (ß-aminoethylether)-N, N'-tetraacetic acid (EGTA) promoted the template activityof solubilized native chromatin, but not that of sonicated ordenatured DNA. The effect of EGTA was reversed by Ca²⁺. Thechromatin reconstituted in the presence of EGTA showed a lowerT_m than the chromatin reconstituted in the presence of Ca²⁺.The relationship between chromatin structure and its templateactivity is discussed in relation to Ca²⁺. (Received August 12, 1985; Accepted December 7, 1985)     

Exploring the Conformational Space of Chromatin Fibers and Their Stability by Numerical Dynamic Phase Diagrams

The three-dimensional structure of chromatin affects DNA accessibility and is therefore a key regulator of gene expression. However, the path of the DNA between consecutive nucleosomes, and the resulting chromatin fiber organization remain controversial. The conformational space available for the folding of the nucleosome chain has been analytically described by phase diagrams with a two-angle model, which describes the chain trajectory by a DNA entry-exit angle at the nucleosome and a torsion angle between consecutive nucleosomes. Here, a novel type of numerical phase diagrams is introduced that relates the geometric phase space to the energy associated with a given chromatin conformation. The resulting phase diagrams revealed differences in the energy landscape that reflect the probability of a given conformation to form in thermal equilibrium. Furthermore, we investigated the effects of entropy and additional degrees of freedom in the dynamic phase diagrams by performing Monte Carlo simulations of the initial chain trajectories. Using our approach, we were able to demonstrate that conformations that initially were geometrically impossible could evolve into energetically favorable states in thermal equilibrium due to DNA bending and torsion. In addition, dynamic phase diagrams were applied to identify chromatin fibers that reflect certain experimentally determined features.