Histones H2a, H2b, H3, and H4 are present in equimolar amounts in chick erythroblasts

Tetranucleosome Interactions Drive Chromatin Folding

The multiscale organizational structure of chromatin in eukaryotic cells is instrumental to DNA transcription, replication, and repair. At mesoscopic length scales, nucleosomes pack in a manner that serves to regulate gene expression through condensation and expansion of the genome. The particular structures that arise and their respective thermodynamic stabilities, however, have yet to be fully resolved. In this study, we combine molecular modeling using the 1CPN mesoscale model of chromatin with nonlinear manifold learning to identify and characterize the structure and free energy of metastable states of short chromatin segments comprising between 4- and 16-nucleosomes. Our results reveal the formation of two previously characterized tetranucleosomal conformations, the "α-tetrahedron" and the "β-rhombus", which have been suggested to play an important role in the accessibility of DNA and, respectively, induce local chromatin compaction or elongation. The spontaneous formation of these motifs is potentially responsible for the slow nucleosome dynamics observed in experimental studies. Increases of the nucleosome repeat length are accompanied by more pronounced structural irregularity and flexibility and, ultimately, a dynamic liquid-like behavior that allows for frequent structural reorganization. Our findings indicate that tetranucleosome motifs are intrinsically stable structural states, driven by local internucleosomal interactions, and support a mechanistic picture of chromatin packing, dynamics, and accessibility that is strongly influenced by emergent local mesoscale structure.

Cell-specific expression of heat shock proteins in chicken reticulocytes and lymphocytes

We have found that chicken reticulocytes respond to elevated temperatures by the induction of only one heat shock protein, HSP70, whereas lymphocytes induce the synthesis of all four heat shock proteins (89,000 mol wt, HSP89; 70,000 mol wt, HSP70; 23,000 mol wt, HSP23; and 22,000 mol wt, HSP22). The synthesis of HSP70 in lymphocytes was rapidly induced by small increases in temperature (2 degrees-3 degrees C) and blocked by preincubation with actinomycin D. Proteins normally translated at control temperatures in reticulocytes or lymphocytes were not efficiently translated after incubation at elevated temperatures. The preferential translation of mRNAs that encode the heat shock proteins paralleled a block in the translation of other cellular proteins. This effect was most prominently observed in reticulocytes where heat shock almost completely repressed alpha- and beta-globin synthesis. HSP70 is one of the major nonglobin proteins in chicken reticulocytes, present in the non-heat-shocked cell at approximately 3 X 10(6) molecules per cell. We compared HSP70 from normal and heat-shocked reticulocytes by two-dimensional gel electrophoresis and by digestion with Staphylococcus aureus V8 protease and found no detectable differences to suggest that the P70 in the normal cell is different from the heat shock-induced protein, HSP70. P70 separated by isoelectric focusing gel electrophoresis into two major protein spots, an acidic P70A (apparent pl = 5.95) and a basic P70B (apparent pl = 6.2). We observed a tissue-specific expression of P70A and P70B in lymphocytes and reticulocytes. In lymphocytes, P70A is the major 70,000-mol-wt protein synthesized at normal temperatures whereas only P70B is synthesized at normal temperatures in reticulocytes. Following incubation at elevated temperatures, the synthesis of both HSP70A and HSP70B was rapidly induced in lymphocytes, but synthesis of only HSP70B was induced in reticulocytes.

Uncoordinated synthesis of histones and DNA by mouse eggs and preimplantation embryos

The temporal coordination of histone and DNA synthesis in mouse eggs and preimplantation embryos were examined. In unfertilized mouse eggs arrested at metaphase II, histone synthesis was observed, but at lower rates than previously reported for fertilized zygotes. Cytosine arabinoside, an inhibitor of DNA synthesis, was used to study the relationship between DNA and histone synthesis during cleavage stages of mouse development. Cytosine arabinoside (50 microM) inhibited by 90% the incorporation of [3H]thymidine into DNA by two-cell embryos and blastocysts. At this concentration, cytosine arabinoside inhibited incorporation of [3H]lysine into blastocyst histones by only 30% and had no effect at the two-cell stage. These results are interpreted to show that DNA synthesis and histone synthesis are not coordinated temporally during early development of the mouse, but may become more so as development proceeds.

Molar proportions and relative rates of synthesis of histones in rat testis

The molar proportions and relative rates of synthesis of histones in normal and hypophysectomized rat testis seminiferous epithelial cells were determined. After hypophysectomy the molar proportions of histones H1, H2B and (H2A + protein A24) in seminiferous epithelial cells of rat testis increased while their corresponding variants TH1-x, TH2B-x and X2 decreased, but the molar proportions of major-class histones (i.e., sum of subfractions) remained relatively constant and similar to the proportions in somatic cells. The apparent molar proportions of the labeled histones, determined immediately after 2-h periods of [3H]leucine incorporation, were much higher relative to H4 than the proportions of total histones determined by dye binding. The values, however, approached the molar proportions of total histones when rats were killed 11 days after the [3H]leucine injection. Two-dimensional gel electrophoresis confirmed that the high initial molar proportions relative to H4 by [3H]leucine incorporation were not due to the possible contamination by highly-labeled non-histone proteins. The specific activity of histone H4 relative to the specific activity of DNA, determined immediately after 3-h periods of [3H]leucine and [14C]thymidine incorporations was similar to the value when rats were killed 13 days after the injections. It is proposed that histones of seminiferous epithelial cells are synthesized disproportionally relative to H4 and in excess of the quantities required for polynucleosome assembly. The excess histones are subsequently displaced or degraded slowly.

Histones H1 and H5: one or two molecules per nucleosome?

We have determined histone stoichiometries in nuclei from several sources by a direct chemical method, with the particular aim of quantitating histone H1 and, in chicken erythrocytes, H5, and of distinguishing between one and two molecules per nucleosome. The four histones H3, H4, H2A and H2B are found in equimolar amounts, as expected for the core histone octamer. The molar ratio of H1 in lymphocyte and glial nuclei is 1.0 per octamer, and in liver nuclei from three species 0.8 per octamer. These results suggest that each nucleosome has one H1 molecule; nucleosomes could acquire two molecules of H1 only at the expense of others containing none. The stoichiometry of H5 in chicken erythrocyte nuclei is similar to that of H1 in other nuclei, being about 0.9 molecules per nucleosome; the H1 also present in these nuclei amounts to 0.4 molecules per nucleosome.

The histone core complex: an octamer assembled by two sets of protein-protein interactions

A protein complex, extracted from calf thymus chromatin with 2 M NaCl, pH 7.5, containing approximately equal molar ratios of histones H2A, H2B, H3, and H4, has been characterized in this study. Gel filtration, sedimentation velocity, and sedimentation equilibrium experiments demonstrate that this complex, known as the core complex, has a molecular weight near that expected for a histone octamer (108 000 for a unit containing two each of the four inner histones) and far exceeding that of a histone tetramer (54 400). This finding suggests that the histone octamer, postulated to be the fundamental histone unit in chromatin, is stable in 2 M NaCl, pH 7.5, in the absence of DNA or chemical cross-linking reagents. In the second part of this study, we demonstrate that the bonds maintaining the octameric complex in 2 M NaCl are weak and distinctly different from the forces stabilizing the H2A-H2B dimer or H3-H4 tetramer. The octamer is dissociated into two H2A-H2B dimers and one H3-H4 tetramer by (i) increasing temperature; (ii) decreasing NaCl concentration; (iii) adding low concentrations of urea or guanidine hydrochloride; and (iv) lowering the pH below 7 or raising it above 10. These findings indicate that the octamer is assembled by two sets-of protein-protein interactions. The first set involves mostly hydrophobic interactions and yields the H2A-H2B dimer and the H3-H4 tetramer subunits. The second set involves the weak association of one H3-H4 tetramer with two H2A-H2B dimers to form an octamer. We suggest that these weak interactions might be derived predominantly from histidine-lysine or histidine-tyrosine hydrogen bonds between the dimer and tetramer subunits.

Yeast inner histones and the evolutionary conservation of histone-histone interactions

The inner histones of the yeast, Saccharomyces cerevisiae, have been isolated and identified by their amino acid compositions. H4 appears to be close to its calf and pea counterparts. H2a, H2b, and H3 have diverged. The isolation of the histones was accomplished by consecutive slab-gel fractionation, and a number of novel features of the method are described. These appear to be generally useful for preparing many types of protein. The binding pattern of the yeast inner histones is identical to the binding pattern for calf and for pea histones. Data on interspecies complexing indicate that the surfaces across which the histones interact are very highly conserved.

Sea urchin nuclei use RNA polymerase II to transcribe discrete histone RNAs larger than messengers

RNA transcribed in isolated sea urchin nuclei and assayed by hybridization to histone genes cloned in E. coli contains sequences homologous to each of the five histone genes. Histone RNA is synthesized exclusively from the same DNA strand which is the template in vivo. Synthesis of the histone gene transcripts is sensitive to alpha-amanitin concentrations which inhibit RNA polymerase II activity. The fraction of histone RNA synthesized in vitro is comparable at two developmental stages to the fraction synthesized in vivo. The nuclear histone transcripts contain sequences homologous to spacer DNA regions present between the coding regions of the 6500 base pair (bp) histone gene repeat unit. The transcription of spacer sequences was demonstrated by hybridization of the nuclear transcripts to subcloned spacer DNA. Although the bulk of the RNA transcripts are greater than 2000 bases long, the histone-specific transcripts are of discrete sizes ranging from 100 bases to about 1100 bases long. Each histone gene hybridizes with at least one of the larger transcripts and with a different subset of smaller RNAs. We do not detect any giant polycistronic transcript spanning the entire histone repeat unit.

Histone composition of nucleosomes isolated from cultured Chinese hamster cells

Nuclei isolated from cultured Chinese hamster cells were treated with micrococcal nuclease and lysed, and the resulting chromatin subunit classes (nucleosomes) were purified by sedimentation and resedimentation through isokinetic sucrose gradients. Nucleosomes isolated from [3H]thymidine-labeled cells were analyzed for DNA size using both polyacrylamide gel and electron microscopic techniques. Nucleosomes isolated from [14C]lysine-labeled cells were analyzed for protein content using a sodium dodecyl sulfate-polyacrylamide gel system. The results from monitoring the [14c]lysine in each protein indicate that, in the nucleosome classes (monomer through tetramer), the molar ratios of histones H2A, H2B, H3, and H4 are equivalent. Furthermore, in each population of the nucleosome classes monomer through tetramer, it was possible to demonstrate that this histone unit (H2A + H2B + H3 + H4) is present, on the average, in the amount of two for monomers, four for dimers, six for trimers, and eight for tetramers. This is direct experimental confirmation of the prediction of R.D. Kornberg [(1974) Science 184, 868] concerning the substructure of chromatin.

A quantitative analysis of histone H1 in rabbit thymus nuclei

The relative quantity of histone H1 in rabbit thymus whole histone was determined to be 17.2% (w/w). This implies that there is, on average, one histone H1 molecule per nucleosome.