DNA folding by histones: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones.

The kinetics of the chromatin core particle reassembly reaction in solution were quantitatively studied under conditions such that nucleohistone aggregation did not occur. Core particles, salt-jumped rapidly by dilution from 2.5 m-NaCl (in which DNA and histones do not interact) to 0.6 m-NaCl (in which core particles are nearly intact), reassemble in two distinct time ranges. Approximately 75% of the DNA refolds into core particle-like structures “instantaneously” as measured by several physical and chemical techniques with dead times in the seconds to minutes time range. The remaining DNA refolds with relaxation times ranging from 250 minutes at 0 °C to 80 minutes at 37 °C; this slow effect cannot be attributed to sample heterogeneity. The fraction of slowly refolding DNA and the slow relaxation time are independent of the core particle concentration. Transient intermediates present during the slow phase of refolding were identified as free DNA and core particle-like structures containing excess histone. Mixing experiments with DNA, histones, and core particles showed that core particle-histone interactions are responsible for the slow kinetics of DNA refolding. Upon treatment of reassembling core particles with the protein crosslinking reagent, dimethylsuberimidate, the slow phase of the reassembly reaction was arrested and a 13 S particle containing DNA and two octamers of histone was isolated. Consistent with the nature of this kinetic intermediate, it is shown that in 0.6 m-NaCl, core particles co-operatively bind at least one additional equivalent of histones with high affinity in the form of excess octamers. Also, core particles continue to adsorb considerably more histones with a weaker association constant of the order 10⁵m^?1 (in units of octamers) to a maximum value of 12 ± 2 equivalents (octamers) per core particle. The sedimentation coefficient increases with the two-thirds power of the molecular weight of the complex, as it would in the case of clustered spheres.A reassembly mechanism consistent with the data is presented, and other simple mechanisms are excluded. In the proposed mechanism, core particles reassemble very rapidly and compete effectively with DNA for histones such that approximately one-third of the particles initially formed are complexed with an excess octamer of histones, and 25% of the total DNA remains uncomplexed. The amount of this unusual reaction intermediate decays slowly to an equilibrium value of about 10%, thereby leaving 9% of the total DNA uncomplexed. Approximate values are calculated for the free energies, rate constants, and two of the activation energies which characterize this migrating octamer mechanism. This mechanism provides a means whereby histone octamers can be temporarily stripped off DNA at a modest free energy cost, approximately 2.6 kcal per nucleosome. Also, the properties of excess histone adsorption by chromatin and octamer migration suggest an efficient mechanism, consistent with observations by others, for nucleosome assembly in vivo during replication.     

Laser Raman identification of an interaction site on DNA for arginine containing histones in chromatin.

Comparisons of the Raman spectra of DNA, chromatin, and complexes of DNA with poly-L-arginine and N-α-acetylarginine have been made. Both in native chromatin and in complexes of DNA with the arginine derivatives there is a marked decreased in the Raman intensity of the 1490±2 cm^?1 band due to guanine. Considerable evidence is presented to show that a decrease in the intensity of the 1490 cm^?1 Raman band of quanine in DNA is strong indication of a hydrogen bond being attached to the N-7 position of quanine. A specific model is presented for the interaction of the arginine residues with the guanine residues in the major groove of DNA. The Raman frequency of the histone Amide 1 band indicates that these protein molecules have a high α-helical content while the phosphate diester stretch frequency of the DNA shows the DNA to be in the B-family.     

Sperm histones and chromatin structure of the "primitive" sea urchin Eucidaris tribuloides

The "primitive" sea urchin Eucidaris tribuloides resembles the advanced sea urchins (euechinoids) in many respects, yet some features of its biochemistry and morphogenesis are more similar to other echinoderms such as starfish or sea cucumbers. Two unique characteristics of the sperm chromatin of all known euechinoids are an extremely long average nucleosomal repeat length and the presence of two male germ-line-specific histone variants, Sp H1 and Sp H2B. Histone composition and nucleosomal repeat length of the sperm chromatin of Eucidaris were compared to those of several euechinoids and a starfish. Eucidaris sperm chromatin contained large H1 and H2B histone variants typical of euechinoids. The H1 was about nine amino acids smaller than Sp H1 of the advanced urchin Strongylocentrotus purpuratus. Its Sp H2B molecules were the same size as in the euechinoids. Peptide maps showed that N-terminal regions of Sp H1 and Sp H2B contained repeating basic amino acid motifs characteristic of euechinoids. The smaller size of Eucidaris H1 is accounted for by a smaller C-terminal region. The repeat length of Eucidaris sperm chromatin was slightly shorter than that of two euechinoids, but significantly larger than starfish, which lacks a large H2B. The Sp H2B gene of Eucidaris was expressed during spermatogenesis in the same cell types as for S. purpuratus. Thus Sp histone subtype expression and chromatin structure in this distantly related echinoid closely resemble the euechinoids. The presence of an Sp H2B and a very long repeat length appear to be characteristic of the echinoids only.     

Photochemical cross-linking of histones to DNA nucleosomes.

Ultraviolet (UV)-induced cross-linking was utilized in order to identify histone-DNA interacting regions in the chromatin repeating unit. Fractionated mononucleosomes which contained 185 base pairs of DNA and a full complement of the histones, including histone H1, were irradiated with light of lambda greater than 290nm in the presence of a photosensitizer. Equimolar amounts of histones H2A and H2B were found, by two independent labeling experiments, to be cross-linked to the DNA. Based on previous finding that the UV irradiation specifically cross-links residues which are in close proximity, irrespective of the nature of the amino acid side chain or the nucleotide involved, our results indicate that the four core histones are not positioned equivalently with respect to the DNA. This arrangement allows histones H2A and H2B to preferentially cross-link to the DNA. A water soluble covalent complex of DNA and histones was isolated. This complex was partially resistant to mild nuclease digestion, it exhibited a CD spectrum similar to that of chromatin, and was found to contain histone H1. These results are compatible with a model which suggests that histone H1, though anchored to the linker, is bound to the DNA at additional sites. By doing so it spans the whole length of the nucleosome and clamps together the DNA fold around the histone core.     

Buoyant density centrifugation of sea urchin embryo chromatin on sucrose-glucose gradient

Unsheard chromatin isolated from sea urchin embryos was submitted to buoyant density centrifugation in sucrose-glucose gradients. The main peak of blastula chromatin was at a density position of 1.299±0.028±0.009 g ml^-1 whereas at gastrula stage a shift to a lower buoyant density position of (1.276±0.021±0.007 g ml^-1) was observed. Besides the main peak, a small band with a density of 1.18 g ml^-1 was noticed. The lighter fraction differed from the heavy one in a higher histone to DNA ratio, a lower proportion of the F-1 histone, and a lower nonhistone to DNA ratio. The most pronounced developmental alterations of proteins were observed at the level of nonhistone protein patterns of the light fractions.     

Stage-specific mRNAs coding for subtypes of H2A and H2B histones in the sea urchin embryo

Phagocytosis, pinocytosis and the surface distribution of concanavalin A (ConA) have been analyzed during mitosis in several mammalian cell lines. Use of the bisbenzimidazole dye, Hoechst 33258, for chromosome staining after gentle fixation made possible the rapid identification and correlation of mitotic phase with surface properties.Phagocytosis of both opsonized and nonopsonized particles is markedly depressed in mitotic cells of the mouse macrophage cell line J774.1. The uptake of opsonized particles (IgG-coated erythrocytes) is Impaired from early prophase through early G1, whereas phagocytosis of non-opsonized particles (latex beads) is restored by telophase. Fluid pinocytosis, determined by the uptake of soluble horseradish peroxidase, is also inhibited during mitosis. Thus peroxidase-containing cytoplasmic vesicles were virtually absent from mid-prophase through telophase in both J774 and Chinese hamster ovary (CHO) cells.Adsorptive pinocytosis of ConA was determined from the different distributions of fluorescence in single cells incubated at 37°C with rhodamine-conjugated ConA (surface and cytoplasmic label), then fixed and further incubated with fluorescein-conjugated anti-ConA (surface only). The separate fluorescence of Hoechst, fluorescein and rhodamine could be optically isolated. In interphase J774 cells, ConA is rapidly internalized into cytoplasmic vesicles. In contrast, ConA is restricted to the plasma membrane from mid-prophase through telophase. In CHO, the depressed pattern of internalization is not fully established until metaphase.The surface distribution of ConA also varied dramatically as a function of mitotic phase. Between mid-prophase and early anaphase, the pattern of surface ConA-receptor complexes is diffuse. Once the cleavage furrow begins to develop, however, ConA moves into the region of the furrow. This was shown in J774, CHO and 3T3 mouse embryonic fibroblasts, and is probably universal. ConA movement into the membrane that overlies the microfilaments of the contractile ring is analogous to similar movements that occur in interphase cells during ConA cap formation and during the development of phagocytic pseudopods. The analogy emphasizes the common functional consequences of microfilament-membrane organization.It is evident that membrane processes which depend upon endocytosis-for example, certain hormone-induced signals-may be interrupted during mitosis. Inhibition of endocytosis thus may be a significant element in the control of cellular activities during mitosis and a strong influence on the properties of the emergent post-mitotic cell.     

Structural differences in the chromatin from compartmentalized cells of the sea urchin embryo: differential nuclease accessibility of micromere chromatin.

The chromatin structure of three cell types isolated from the 16-cell stage sea urchin embryo has been probed with micrococcal nuclease. In micromeres, the four small cells at the vegetal pole, the chromatin is found to be considerably more resistant to degradation by micrococcal nuclease than chromatin in the larger mesomere and macromere cells which undergo more cellular divisions and are committed to different developmental fates. The micromeres show an order of magnitude decrease in the initial digestion rate and a limit digest value which is one third that of the larger blastomeres; both observations are suggestive of the formation of a more condensed chromatin structure during the process of commitment, or as the rate of cell division decreases. The decreased sensitivity to nuclease for micromeres is similar to results reported for sperm and larval stages of development.     

Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins.

An automated method of running a tandem sequence of oligonucleotide affinity columns was used to purify factors that interact specifically with cis-regulatory sites of the CyIIIa cytoskeletal actin gene of the sea urchin embryo (Strongylocentrotus purpuratus). The method allows quantitative enrichment in a single chromatographic run of up to 12 different sequence-specific DNA binding proteins, each of which may then be readily purified to homogeneity by methods such as preparative gel electrophoresis. The affinity chromatography and identification of six different CyIIIa-regulatory factors is described, and the general utility of the method is discussed.     

Fibronectin in the developing sea urchin embryo

The presence of fibronectin in developing sea urchin embryos was studied uing immunofluorescence staining. The fluorescence pattern indicates that fibronectin is found on the cell surfaces and between cells in the blastula and gastrula stages, indicating that it plays a role in cell adhesion. Its presence on invaginating cells also suggests its involvement in morphogenesis during early development.     

Determination and morphogenesis in the sea urchin embryo

The study of the sea urchin embryo has contributed importantly to our ideas about embryogenesis. This essay re-examines some issues where the concerns of classical experimental embryology and cell and molecular biology converge. The sea urchin egg has an inherent animal-vegetal polarity. An egg fragment that contains both animal and vegetal material will produce a fairly normal larva. However, it is not clear to what extent the oral-aboral axis is specified in embryos developing from meridional fragments. Newly available markers of the oral-aboral axis allow this issue to be settled. When equatorial halves, in which animal and vegetal hemispheres are separated, are allowed to develop, the animal half forms a ciliated hollow ball. The vegetal half, however, often forms a complete embryo. This result is not in accord with the double gradient model of animal and vegetal characteristics that has been used to interpret almost all defect, isolation and transplantation experiments using sea urchin embryos. The effects of agents used to animalize and vegetalize embryos are also due for re-examination. The classical animalizing agent, Zn2+, causes developmental arrest, not expression of animal characters. On the other hand, Li+, a vegetalizing agent, probably changes the determination of animal cells. The stability of these early determinative steps may be examined in dissociation-reaggregation experiments, but this technique has not been exploited extensively. The morphogenetic movements of primary mesenchyme are complex and involve a number of interactions. It is curious that primary mesenchyme is dispensable in skeleton formation since in embryos devoid of primary mesenchyme, the secondary mesenchyme cells will form skeletal elements. It is likely that during its differentiation the primary mesenchyme provides some of its own extracellular microenvironment in the form of collagen and proteoglycans. The detailed form of spicules made by primary mesenchyme is determined by cooperation between the epithelial body wall, the extracellular material and the inherent properties of primary mesenchyme cells. Gastrulation in sea urchins is a two-step process. The first invagination is a buckling, the mechanism of which is not understood. The secondary phase in which the archenteron elongates across the blastocoel is probably driven primarily by active cell repacking. The extracellular matrix is important for this repacking to occur, but the basis of the cellular-environmental interaction is not understood.(ABSTRACT TRUNCATED AT 400 WORDS)     

Isolation and properties of the initiation of DNA replication in the sea urchin embryo

Using the instability of replication loops as a method for the isolation of double-stranded nascent DNA from embryos of the sea urchin Strongylocentrotus intermedius, extruded DNA enriched for replication origins was obtained. The average length of the fragments of the DNA of this fraction was estimated to be about 800 base pairs. The origin-enriched nascent DNA strands were assayed for the presence of inverted repeats. The results show that the origin-enriched DNA is also enriched in inverted repeats. The bulk of palindromes in the total nuclear DNA was estimated to be 200 base pairs in length and from the origin-enriched DNA-150 base pairs.     

Metrizamide density gradients of sea urchin chromatin: fractions rich and poor in nascent DNA.

A crude, lightly sheared chromatin preparation obtained from a mixture of [methyl-3H] thymidine pulse and [2-14C] thymidine long-labeled sea urchin embryos (swimming blastulae), was centrifuged in metrizamide to form an isopycnic gradient. The buoyant density of the 3H pulse labeled chromatin was slightly higher than that of the 14C labeled bulk chromatin. The 3H/14C ratios in the higher and lower density regions of the overlapping radioactivity peaks, indicated the presence of fractions rich and poor in nascent DNA in these two density regions. After 15 min chase, the difference disappeared, indicating that the chromatin fractions with nascent DNA have a half-life shorter than 15 min.     

Fibronectin-binding acid polysaccharide in the sea urchin embryo

Summary A novel fibronectin-binding acid polysaccharide (FAPS) was isolated from embryos of the sea urchin. Binding of FAPS to fibronectin was quantitatively measured at physiological pH and ionic strength by two different assay systems. Immunofluorescent studies revealed that FAPS is localized in the extracellular matrix surrounding the mesenchyme cells and primitive gut of middle gastrula. Sea urchin fibronectin was also detected in the extracellular matrix surrounding mesenchyme cells and the cells surrounding the blastopore. When a monoclonal antibody to FAPS (anti-FAPS) was microinjected into the blastocoel, more than one pair of triradiate spicular rudiments was formed and the malformation of spicules was induced. Armless and deformed larvae were also induced by anti-FAPS. FAPS may regulate the number, length, position and direction of spicules. These results implicate the extracellular matrix of the blastocoel in the complex process of differentiation of mesenchyme and the formation of spicules.