Stepwise removal of histones from native deoxyribonucleoprotein by titration with acid at low temperature and some properties of the resulting partial nucleoproteins

Age-dependent changes in the phosphorylation of nuclear proteins of submandibular glands in isoproterenol-treated rats

Age-dependent changes in the regulation of the phosphorylation of nuclear proteins were investigated in relation to DNA synthesis in rat submandibular glands after injection of isoproterenol (IPR). The level of phosphorylation of nuclear proteins in the tissue increased rapidly after birth, reaching a maximum at 4 weeks, and then decreased to the level of 52-week-old rats. The level of protein kinase activity in nuclei varied in parallel with that of phosphorylation of nuclear non-histone proteins after birth. The time after the injection of IPR required to initiate the phosphorylation of nuclear non-histone proteins of rat submandibular glands, which occurs prior to the onset of RNA synthesis that precedes the replication of DNA, increased with age. These results suggest that this delayed onset of phosphorylation plays a regulatory role in cell proliferation and cell function during aging.

The capsid protein of Semliki Forest virus has clusters of basic amino acids and prolines in its amino-terminal region

The amino acid sequence of the capsid (C) protein was deduced from the nucleotide sequence of the C gene. This part of the viral 42S RNA genome was transcribed into double-stranded cDNA. The cDNA was cloned in the Escherichia coli chi 1776-pBR322 host-vector system and then the base sequence was determined with the technique described by Maxam and Gilbert. The amino acid sequence of the C protein shows a clustering of basic amino acids and prolines within the first 110 amino acids.

On mechanisms determining the interrelationships between DNA and histone components of chromatin

The relative affinity of histones for DNA was studied by the analysis of competitive histone binding to DNA in whole histone/DNA mixtures at physiological and low ionic strengths as well as in water. Use of polyphosphate in similar experiments, as a model of DNA deprived of hydrophobic functional groups allowed us to reject the hypothesis that hydrophobic DNA-histone interaction plays a decisive role in the determination of the relative affinity of histones for DNA, because the orders of histone preference for DNA and for polyphosphate were the same. The relative histone affinity for DNA does not depend on the secondary structure of DNA or on the ionic strength of salt solutions, though the differences in the histone affinities for DNA decrease on lowering the salt concentration. The binding orders of the first and the last molecules of histone type to DNA, studied at various DNA/histone ratios in the medium of physiological ionic strength, are the following: H3+H4, H2A+H2B, H1 and H3+H4, H2A, H2B, H1. In water the binding orders of the first and the last histone molecules to DNA are identical: H3+H4, H2A, H2B+H1. It is concluded that the relative histone affinity for DNA in water/salt solutions is determined by non-ionic interactions between histones bound to DNA. The folding of DNA induced by histone-histone interaction seems to lead to the increase in the correlation between amino acid residues in the histone regions bound to DNA and the ionic DNA-histone interaction becoming stronger.

Identification of nonhistone chromatin proteins in chromatin subunits

Rat liver chromatin was digested by micrococcal nuclease. More than 80% of the enzyme-digested chromatin could be recovered after centrifugation. Treatment with sodium deoxycholate and Triton X-100 at concentrations of 0.5% in the final chromatin suspension gave a higher recovery. Chromatin subunits were fractionated on a 5-30% linear sucrose density gradient. Approximately 35% of the chromatin subunits could be recovered from the gradient. Chromatin subunits and their DNA fragments were identified by gel electrophoresis and ultracentrifugation. The presence of nonhistone chromatin proteins (NHCP) in chromatin subunits was demonstrated by the following criteria: (i) Quantitative analysis showed that the mass ratio of histone to NHCP, in the presence or absence of detergents, was 1:0,25 or 1:0.1, respectively. (ii) After the removal of acid-soluble protein from the subunits, it was found that most of the phenol-soluble NHCP were similar to total chromatin NHCP. However, four major fractions of these phenol-soluble NHCP were found to be enriched in the subunits as identified by two-dimensional polyacrylamide gel electrophoresis. (iii) Experiments using an exchange of isotope-labeled and nonlabeled chromatin showed that NHCP were tightly bound to the chromatin subunits.

Removal of histone H1 exposes a fifty base pair DNA segment between nucleosomes

Micrococcal nuclease has been used to prepare chromatin from HeLa cells and to probe the structure of HeLa chromatin under various ionic conditions and after the removal of chromatin proteins by salt extraction. The results suggest that (1) HeLa chromatin DNA exists as 150-160 base pair beads interspersed with 40-50 base pair bridges;(2) the bead and bridge conformation exists at physiologic salt concentrations; and (3) removal of histone H1 renders the 40-50 base pair bridge, but not the 150-160 base pair bead, more nuclease susceptible.

Locations of chromosomal proteins in polytene chromosomes

D1, a nonhistone chromosomal protein rich in both basic and acidic amino acids, has been localized at a limited number of specific loci in polytene chromosomes of Drosophila melanogaster. H2B, a nucleosomal histone, and H1, a nonnucleosomal histone, are both found throughout most chromosomal regions.

Fractionation of chick oviduct chromatin. Nuclease-resistant deoxyribonucleic acid

Chromatin isolated from several chick tissues was treated with micrococcal nuclease. A limited degree of tissue specificity of chromatin DNA resistance to nuclease digestion was observed. No difference in the extent of nuclease resistance of chromatin DNA was detected during oestrogen-induced oviduct differentiation. This suggested that the amount of non-histone chromosomal protein does not play an important role in the sensitivity of chromatin DNA to nuclease digestion. Studies of nuclease resistance of chromatin DNA after dissociation and reconstitution of chromatin proteins and ethanol extraction of chromatin indicate that the histones protect the DNA from nuclease attack. Slow thermal denaturation of nuclease-resistant DNA suggests that the protected DNA sequences may be (A+T)-rich, and the (G+C)-rich satellites present in total chick DNA are sensitive to nuclease.

Absence of histone F1 in a mitotically dividing, genetically inactive nucleus

Histones were extracted from macro- and micronuclear chromatin of the ciliated protozoan Tetrahymena pyriformis. Conditions that resulted in macronuclear chromatin containing large amounts of histone F1 yielded micronuclear chromatin in which this histone was absent. Evidence is presented indicating that the absence of F1 from micronuclei is not a preparative artifact and that histone F1 is replaced by other histone fractions. Since micronuclei divide mitotically, while macronuclei divide amitotically, these results suggest that histone F1 and its phosphorylation do not play an indispensable role in the process of mitotic chromosome condensation, in chromosome replication, or in the separation of newly synthesized chromatids.

Selective removal of histones from calf-thymus nucleohistone with sodium dodecylsulfate

Calf-thymus nucleohistone studied by a newly developed ;SDS gradient' centrifugation technique showed that histones dissociate sequentially when treated with increasing concentrations of sodium dodecylsulfate. Histones F2a1 and F2a2 were dissociated first at about 0.03% sodium dodecylsulfate, and F1 was removed lastly by the highest concentration of sodium dodecylsulfate (0.06% or more). A DNA-histone F1 complex, which consisted of DNA and all of the histone F1 and completely lacked other histones, was obtained by sedimenting nucleohistone through 0.05% sodium dodecylsulfate. Results of equilibrium gel filtrations in 0.05% sodium dodecylsulfate revealed that the binding of sodium dodecylsulfate to nucleohistone caused new binding sites to be available for the detergent which presumably was accompanied with dissociation of histones from DNA. This result indicates that no redistribution of histone F1 on DNA should occur in the presence of 0.05% sodium dodecylsulfate.

Nucleotide sequence analysis with polynucleotide kinase and nucleotide "mapping" methods. 5'-Terminal sequences of deoxyribonucleic acid from bacteriophages lambda and 424

The polynucleotide kinase reaction was used in analyses of complex mixtures of oligodeoxynucleotides which were fractionated by various two-dimensional nucleotide ;mapping' procedures. Parallel ionophoretic analyses on DEAE-cellulose paper, pH2, and AE-cellulose paper, pH3.5, of venom phosphodiesterase partial digests of 5'-terminally labelled oligonucleotides enabled the sequence of the nucleotides to be deduced uniquely. A ;diagonal ionophoresis' method has been used with mixtures of nucleotides. Application of these methods to 5'-terminally labelled DNA from bacteriophage lambda gave the terminal sequences pA-G-G-T-C-G and pG-G-G-C-G. Identical 5'-terminal sequences were found with DNA from bacteriophage 424.

Polynucleotides associated with histone preparations

Histone fractions prepared from various sources by acid extraction or by salt dissociation contained small quantities of ribo- and deoxyribo-nucleotides. These nucleotides were small and heterogeneous and were efficiently removed from histone preparations by ionexchange chromatography. They probably represent contaminants, rather than uniquely complexed nucleotides, of all the histone preparations.

Transcription of brain chromatin by ribonucleic acid polymerases from brain nuclei and from Escherichia coli

1. Transcription of ox brain chromatin by brain nuclear RNA polymerase II and Escherichia coli RNA polymerase was studied. 2. The soluble chromatin prepared from brain nuclei contained DNA, RNA, histone and non-histone proteins. Such chromatin preparations did not display any endogenous RNA polymerase activity, when assayed in the presence of concentrations of KCl as high as 0.4m. 3. The chromatin-templated activity of brain nuclear polymerase II was stimulated by KCl, with an optimum around 0.25m. 4. The template activity of brain chromatin for brain nuclear polymerase II and E. coli enzyme was about 20-25% of that of pure DNA. This greatly repressed templatecapacity of chromatin was probably due to the acid-soluble chromosomal proteins. 5. Brain nuclear polymerase II was 3-4 times more active with dehistonized chromatin than with pure DNA as template, whereas bacterial enzyme was almost equally active with either of these two templates, reflecting the specificity of the transcriptional control mechanisms in mammalian cells.

The structure of chromatin

The DNA in chromatin of isolated thymus nuclei, and in two different preparations of deoxyribonucleoprotein extracted from chromatin, has been digested with DNase. By variation of the time of reaction and the concentration of enzyme, and by comparison of the action of the enzyme on (protein-free) DNA with its action on DNA complexed with protein in chromatin and deoxyribonucleoprotein, it was found that most, if not all, of the DNA is linked to protein. The linkage is loose, as shown by the fact that all the DNA is accessible to the enzyme; however, the wide variations in accessibility in a given complex show that the looseness of the DNA-protein link varies considerably. Accessibility of DNA in one type of deoxyribonucleoprotein preparation is greater than it is in chromatin, while in the other type it is less than in chromatin.