Studies on the reactive properties of histone amino groups: reactivities of free histones and histones in chromatin as a function of ionic strength.

The reactivity of the amino groups of the five histones towards acetic anhydride has been measured and with the exception of histone IIb2 the reactivities are very similar to those of exposed lysines with an average pK of 9.5. In addition the reactivities of these groups from 0.20 to 1.0 M NaCl and the reactivity of a peptide containing lysines 5, 8, 12 and 16 of histone IV have been measured in chromatin. It is concluded that at the lower ionic strengths the large proportion of the amino groups are buried for both the histones and the region of histone IV studied. Data obtained from the measurement of the reactivity of standard proline compounds and from a pH and ionic strength study indicate that the N-terminal proline of histone IIb2 is exposed.     

Complete displacement of somatic histones during transformation of spermatid chromatin: a model experiment.

Displacement of histones from calf thymus chromatin has been studied in an attempt to postulate the mechanisms involved in the total removal of somatic-type histones during transformation of spermatid chromatin. When chromatin is saturated with protamine (protamine/DNA, 0.5), histone I becomes displaceable at 0.15-0.3 M NaCl, suggesting that direct replacement by highly basic sperm histone could be a mechanism for its removal. While histone I is the only histone which is extensively degraded upon incubation of chromatin and, therefore, proteolysis might provide an additional mechanism for the removal of this histone, acetylation of chromatin by acetic anhydride greatly increases suscpetibility of histones IIb1, IIb2, and III to the chromosomally associated protease. These histones are extensively degraded and displaced from the DNA upon incubation of the acetylated chromatin. Although histone IV is not appreciably degraded, the proteolytic removal of acetylated histone III from chromatin weakens the interaction of acetylated histone IV to the DNA, and this histone becomes dissociable at 0.3 M NaCl. A comparison of the extent of chemical acetylation of individual histones observed in this investigation with that of enzymatic acetylation which can be achieved in vivo suggests that acetylation and proteolysis could be a mechanism for the removal of histone IIb2 and III. The displacement of histones IIb1 and IV could be explained on the basis of decreased binding to DNA as a result of their acetylation together with the proteolytic removal of their respective partner histones, IIb2 and III.     

Unmasking of histone amino groups in chromatin at high pH.

The reactivity of the amino groups of histones in chromatin towards acetic anhydride was determined as a function of pH. In the pH range 7-10 the vast majority of amino groups in all five histones are buried. However, at higher pH values some of the histone amino groups become exposed, and the higher the lysine:arginine ratio for the histone the greater was the degree of unmasking observed. At pH 11.8 histone I appears to be completely dissociated, histones IIB1 and IIb2 have approx. 55% of the amino groups unmasked, and histones III and IV have approx. 25% of the amino groups unmasked.     

In vitro acylation of the ϵ-amino group of l-lysine in calf thymus histones by the carcinogen, β-propiolactone

We had previously reported that the carcinogen, β-propiolactone (BPL) reacted in vitro with histones in whole mouse skin chromatin and that among the histone classes BPL was preferentially bound to the lysine-rich histones H1 and H1°. In order to determine if in vitro reaction of BPL with calf thymus histones resulted in binding of BPL to l-lysine, we synthesized the model compounds ?-N-(3-hydroxypropionyl)lysine (HPL) and ?-N-(2-carboxyethyl)lysine (CEL) from BPL and l-lysine. The α-amino group of l-lysine was protected from reaction with BPL by the formation of a copper chelate.Structures were assigned on the basis of infrared spectra, pKa values and chemical analyses. BPL was reacted in vitro with calf thymus histones and the BPL-reacted calf thymus histones and control calf thymus histones were digested with trypsin followed by pronase. The respective digests were each chromatographed on a column of AA-15 cation-exchange resin. The elution profiles of the two digests were very similar except for the appearance of a new ninhydrin-positive peak (NNPP) in the eluate of the trypsin-pronase digest of BPL-reacted calf thymus histones. When compounds HPL and CEL were added to the trypsin-pronase digest of control calf thymus histones and the mixture chromatographed on AA-15, both compounds were resolved from the other peptide (or amino acid) peaks. HPL was eluted in the same fractions as NNPP, HPL and NNPP exhibited identical R_F values on silica gel TLC with acidic, alkaline and neutral solvents. CEL was not identified as a product of the reaction between BPL and calf thymus histones.     

Modification of histone binding in calf thymus chromatin and in the chromatin-protamine complex by acetic anhydride.

A relationship between side-chain modification of histones and their displaceability from DNA has been investigated using calf thymus chromatin which was chemically acetylated with acetic anhydride. When the chromatin is treated with increasingly higher concentrations of the reagent, histones become acetylated to an increasingly greater extent, attaining the modification at 23-24 sites for histone I, 5-6 for IIb1, 9-10 for IIb2, 5-6 for III and 3-4 for IV. As the chromatin becomes more acetylated, NaCl concentrations required for histone removal are lowered. Saturation binding of protamine does not bring about either an increase in the number of acetylation sites of histones in chromatin or a decrease of the NaCl requirement for dissociation of the acetylated chromatins. A comparison of the present results with the extents of histone acetylation known to occur enzymatically in vivo indicates that the complete removal of somatic histones during transformation of chromatin in spermiogenesis cannot be explained on the basis of decreased binding of the histone to DNA by acetylation or by a combination of acetylation and protamine binding, suggesting that the displacement process may require some additional processes.     

Separation and properties of an H2B histone variant from the sperm chromatin of the sea urchin Sphaerechinus granularis

The purification and the physico-chemical characterization of one of the two H2B histone variants from the sperm of the sea urchin Sphaerechinus granularis are reported. The molecule shows, in addition to a distinctive molecular weight value, an amino acid composition different both from that of calf thymus H2B histone and from those of H2B histones from chromatin of sperm and embryos of other sea urchins. Circular dichroism and fluorescence data are discussed in comparison to those of calf thymus H2B.     

Histones from spermatozoa of the horseshoe crab

It is shown that histones are the nuclear proteins present in spermatozoa of the horseshoe crab Limmulus polyphemus, an arthropod which is considered a living fossil. They have been characterized and found to be closely related to calf thymus histones. The only difference is the presence of an additional histone in small amounts (2?3% of the whole histones) which has intermediate properties between H1 and H2b.     

The role of H2B histones from the sea urchin sperm in the formation of supranucleosome structures

The structural role of histone H2B from sea urchin sperm (H2Bsp) has been examined in experiments on reconstitution of chromatin from DNA and core histones taken in three variants: (1) four core histones from sea urchin sperm; (2) four core histones from calf thymus; (3) (H3, H4, H2A) from calf thymus and H2Bsp. It is shown that H2Bsp when present in reconstituted chromatin induces its aggregation. Fidelity of the reconstitution of nucleosomes has been tested using DNase I probe, one- and two-dimensional electrophoresis and electron microscopy. The reconstitutes that contain H2Bsp appear under electron microscope mainly as regular closely spaced large granules, about 450 A in diameter, which are very similar to the granules found in "native" sea urchin sperm chromatin. The reconstitutes formed by four core histones from calf thymus appear as randomly arranged particles, about 100 A in diameter. We conclude that histone H2Bsp participates in interactions between nucleosomes and is involved in the formation of the condensed supranucleosomal structure in sea urchin sperm chromatin.     

A study of histones in amoeba nuclei by indirect immunofluorescence method.

Nuclear proteins of four species of free-living Amoebidae (Amoeba proteus, A. discoides, Chaos carolinensis and Polychaos dubia) have been studied by indirect immunofluorescence technique using specific antisera to H1, H2A, H2B, H3 and H4 histone fractions from the calf thymus. It has been shown that the nuclei of the species examined have all these five histone fractions. However, the degree of similarity between homologous fractions from amoebae and the calf thymus varies and can be expressed in terms of immunological distance. Immunological differences between amoebic and calf thymus histones are the most pronounced in H1, being least in H3 and H4. Judged by its immunochemical characteristics, the histone fraction H2A from P. dubia is closer to the corresponding fraction from the calf thymus than is H2A from the other three amoeba species.     

Relationships of Histones to RNA Synthesis in Plant Tissues

The RNA-synthesizing activity of the tissue, template activity of the chromatin, histones and other parameters were analyzed for young leaves, senescent leaves and the pith tissue of tobacco. The amount, of RNA, DNA and the extent of incorporation of ³²P into RNA was much lower in old leaves and the pith tissue than in young leaves. Furthermore, the ³²P sucrose density gradient patterns of RNA from the three tissues were very different. In old leaves, the label was found mostly in low molecular weight RNA region, presumably as a result of degradation of RNA by soluble and chromatin-associated ribonucleases which were higher in old leaves. — In addition to significant differences in the composition of chromatin, large differences in the ratios of F_I : F_II : F_III : : histone fractions from the three tissues were noted and the fully differentiated old leaves and the pith tissue had proportionately more F_IIand F_III histones than the less differentiated young leaves. The F_III histone of tobacco differed from that of pea and calf thymus in having lys/arg = 1.2. — Although some correlation between RNA-synthesizing activity of the tissue, template activity of chromatin and the histone composition was noted for the pith tissue and the young leaves, the situation with old leaves was more complicated, probably due to the occurrence of chromatin-associated deoxyribonuclease and involvement of other factors which may also effect RNA synthesis.     

Changes sperm culei during sperimogensis and epidymal maturation.

An antibody specific to histone F2b of calf thymus was prepared by using the highly purified histone fraction in addition to antibodies against histones F1 and F2a1, as reported previously. The nuclear staining pattern obtained with anti-histone F2b antibody was compared to those obtained with anti-histone Fl and F2a1 antibodies in cultured hamster fibroblasts, both by immunofluorescence and immunoperoxidase. The nuclear staining patterns with each anti-histone antibody obtained by immunoperoxidase were almost completely the same as those obtained by immunofluorescence. Nuclear staining patterns with anti-F2b antibody were speckled in appearance with a faint staining of the nuclear membrane. These findings were different from the results obtained with anti-F1 antibody and with anti-F2a1 antibody. These results suggest the possibility that these three histones are located in different chromatin states.     

Sea urchin sperm DNP. I. Chemical composition and template properties of DNP

Electrophoretic mobility, amino acid composition and salt dissociation of histones isolated from sperm of sea urchin Strongylocentrotus intermedius and calf thymus cells were studied. The special arginine-rich histone fraction (I) has been observed in sea urchin sperm chromatin, this fraction being absent in calf thymus chromatin. Dissociation of lysine-containing histone fractions from sea urchin chromatin occured in the range of 0.7 to 1.0 M NaCl concentrations. H1 of calf thymus chromatin was totally extracted with 0.6 M NaCl. In the course of a further increase of salt concentrations (up to 1.5 M NaCl) a practically total extraction of histones from sperm chromatin was observed, while about 20% of proteins remained bound to DNA in thymus chromatin after extraction with 2.0 M NaCl. The template activity of non-extracted DNP preparations from urchin sperm was equal to 2-3% of that of totally deproteinized DNA. The template activity of DNP gradually increased at protein extraction from DNP preparations. The hybridization capacity of RNA transcribed on partially dehistonized DNP templates in vitro also increased.     

Proteolytic digestion of histones indicates that the nucleosomes of nuclei and of sheared chromatin are similar

Calf thymus nuclei were treated with trypsin, chymotrypsin or Pronase, and the rate of digestion of the various histone fractions was determined. The results differed from those obtained by digestion of DNA-free histones with the same set of enzymes but were identical to those obtained by digestion of calf thymus chromatin. Because these enzymes have such different specificities, the results of these digestions indicate that the histone fractions have similar locations in the chromosomal substructures of nuclei and chromatin, $\text{i.e.}$ that the structure of the nucleosomes which exist within nuclei is not changed markedly when chromatin is isolated from nuclei by a method which involves shearing.     

Heterogeneity of the histone-containing chromatin in sea cucumber spermatozoa : Distribution of the basic protein Φ0 and absence of non-histone proteins

Nuclei of spermatozoa of the sea cucumber Holothuria tubulosa contain the five somatic-type histones plus a sperm-specific histone H1 and a unique basic protein ₀, which is related to H1 in amino acid composition. No proteins of the High Mobility Group (HMG) type have been detected. The structure of this chromatin has been probed by nuclease digestion. Its behaviour is anomalous, since two distinct fractions of chromatin are recovered from these spermatozoa, which differ either in the presence or absence of the sperm-specific proteins H1 and ₀. This heterogeneous distribution is not found in conventional materials, such as calf thymus or chicken erythrocytes. Proteins H1 and ₀ are not uniformly distributed and may be localized in special regions of chromatin. Fragments containing long stretches of nucleosomes lacking both proteins can be recovered. At the same time, the chromatin fractions which contain these two proteins are shown to be less soluble. When an extensive digestion of chromatin is carried out yielding only nucleosomes and small oligomers, the H1 and ₀ proteins redistribute themselves on chromatin, the two proteins acting in a cooperative fashion in this process. Cross-linking experiments carried out in whole cells indicate a proximity of ₀ and H1, whereas no crosslinks have been detected between ₀ and any of the four nucleosomal histones. The ₀ protein may thus play a role similar to histone H1 and be only loosely associated with nucleosomal histones, but contribute to the structuration of chromatin during spermiogenesis.     

Modification of the lysine residues of histones H1 and H5: Effects on structure and on the binding to chromatin

The extensive modification of histone H1 from calf thymus with the amino-group reagent dimethylmaleic anhydride (over 35 lysine residues modified per molecule) produces no effect on its secondary structure detectable by circular dichroism (far UV). Fluorescence and circular dichroism (near-UV) of the modified histone show variations in the local environment of its sole tyrosine residue. These changes are reversed on regeneration of the modified amino groups. While histone H1 is easily dissociated with this reagent from calf thymus or chicken erythrocyte chromatin, a much stronger treatment is needed to liberate histone H5 from erythrocyte chromatin. This difference appears to be related to the higher arginine content of histone H5.     

Affinity of chromatin constituents for isopeptidase

Isopeptidase is a novel eukaryotic enzyme that cleaves a structural chromatin protein, A24, stoichiometrically into H2A and ubiquitin. To understand the rapid turnover of ubiquitin in mitosis as wells as the high specific activity of the enzyme associated with metaphase chromosomes, attempts were made to determine chromatin constituents that show high affinity for this enzyme. Endogenous protease-free isopeptidase was prepared from calf thymus and applied to a Sepharose 4B affinity column on which histones, DNA, NHCP and ubiquitin were respectively immobilized. The enzyme proved to bind only histones. To further determine which of the histone fractions is involved, affinity columns with each histone fraction were also used. The enzyme showed affinity for all histone fractions. However, the strength of affinity varied in the order H2A>H³ H2B≥H4?H1, being inversely correlated with the ratio of basic/acidic amino acids in these molecules. These results suggest that the turnover of A24 in mitosis is controlled, at least in part, by the affinity of enzyme for histones, and also that such affinity is caused by a mechanism which cannot be explained simply by the electrostatic interaction between negatively charged enzyme molecules and positively charged histones.     

Modification of histone binding in calf thymus chromatin by protamine.

When calf thymus chromatin is incubated with protamine, the protein binds to DNA, forming a chromatin-protamine complex. The binding reaches a saturating level at the weight ratio of protamine to DNA of approximately 0.5. Although the saturated binding of protamine to DNA does not cause major displacement of histones from calf thymus chromatin, examination of the dissociation profiles by salt in combination with urea of protamine-treated chromatin shows that the histone-DNA interactions are markedly altered by such binding. The dissociation of histones from the chromatin-protamine complex requires less NaCl but the same concentration of urea as that for untreated chromatin, suggesting that the electorstatic interactions between the histones and DNA are decreased as a result of protamine binding. When protamine concentration is increased beyond that required for saturated binding to DNA during in vitro exposure of calf thymus chromatin to protamine, lysine-rich histone is completely displaced.     

Increase in initiation sites for chromatin directed RNA synthesis by acetylation of chromosomal proteins.

Treatment of rat liver chromatin with 0.7 mM acetic anhydride (1) leads to an approximately twofold increase in initiation sites for DNA-dependent RNA polymerase from $\text{E.}\text{coli}$. With reconstituted chromatin, in which only the histone moiety was acetylated, again a twofold increase in initiation sites could be observed, compared to control chromatin which had undergone the dissociation and reassociation procedure, but which had not been exposed to acetic anhydride.     

Chemically induced gene activation: Selective increase in DNAase I susceptibility in chromatin acetylated with acetyl adenylate

Treatment of calf thymus chromatin with acetyl adenylate under appropriate conditions produces acetylation of histones. The pattern of histone acetylation obtained is similar to that produced $\text{in}$$\text{vivo}$. The acetylated chromatin shows increased sensitivity to DNAase I but no increased sensitivity to Staphylococcal nuclease. These digestion patterns are similar to those observed in active genes.