Solubilization of chromatin by an endogenous enzymic Ca2+, Mg2+-dependent factor. Activity of residual chromatin]

An endogenous Ca2+, Mg2+-dependent factor of enzymic nature (apparently an endonuclease) digests a part of chromatin in the rat liver nuclei producing DNA fragments of an uniform size. After 60 min of incubation at 15 degrees C and pH 7.50 in the presence of 5 mM MgCl2 and 2 mM CaCl2 87-93% of the total chromatin becomes soluble. The insoluble chromatin however contains 70-85% of the in vivo newly synthesized RNA. In regenerating liver the proportion of the insoluble residual chromatin increases while the radioactivity of the newly synthesized DNA in this fraction is highest. Residual chromatin can be solubilized by ultrasonic treatment only. The Ca2+, Mg2+-dependent dissolving factor is not present either in brain or in PMN leucocyte nuclei.     

Distribution of estrogen receptors in subfractions of hen oviduct chromatin.

Hen oviduct chromatin was digested with DNase II and separated into two fractions. The MgCl2 insoluble chromatin fraction (43% of the total DNA) was enriched in nucleosome-like particles, which sedimented at 11 S and contained 185 base pairs of DNA. The MgCl2 soluble chromatin fraction (5% of the total DNA) was characterized by 5 S and 14 S peaks in sucrose gradients; Estrogen receptors in the chromatin fractions were labelled with [3H] estradiol using the steroid exchange assay. The concentration of receptors in the MgCl2 soluble chromatin was 4;5 times higher than that in the MgCl2 insoluble chromatinmin sucrose gradient analysis the 11 S particles displayed a negligible specific radioactivity suggesting that estrogen receptors mainly bind to extranucleosomal chromatin.     

The organization of oligonucleosomes in yeast

We have developed a method of preparing yeast chromatin that facilitates the analysis of nucleoprotein organization. Yeast chromatin, isolated as an insoluble complex, is digested with micrococcal nuclease and fractionated into major insoluble and soluble fractions. No nucleosomal repeat is seen early in digestion for the insoluble fraction. Nucleosomal complexes of the soluble fraction are excised by nuclease in a distinctive non-random pattern; they are markedly depleted in mononucleosomes. When we analyze the soluble material by high resolution native electrophoresis, we find that the nucleoproteins resolve into two bands for each DNA multimer of the nucleosomal repeat. Our results suggest that there are structural similarities between bulk yeast chromatin and chromatin configurations found in transcribing genes of complex eukaryotes.     

Fractionation of micrococcal nuclease-digested chromatin solubilized at physiologic ionic strength

When mouse brain nuclei are optimally digested with micrococcal nuclease, most of the chromatin is soluble in a 180 mM salt/1 mM EDTA buffer [1]. At this ionic concentration, chromatin maintains its native structure [2]. In an attempt to selectively extract different fractions of chromatin from digested nuclei, we have examined the differential solubility of chromatin in the 180 mM salt buffer containing concentrations of MgCl2 ranging from 2 to 0 mM. The results suggest that digested chromatin may be fractionated into specific soluble chromatin fractions which correspond to nuclease-sensitive chromatin, bulk chromatin, and heterochromatin. These soluble fractions have a high molecular weight (up to 20 kbp), and contain a full complement of histones as well as a complex assortment of non-histone proteins. The residual insoluble fraction may be equivalent to a native, nuclear matrix-bound chromatin fraction.     

Distribution of estradiol receptor and vitellogenin gene in chick liver chromatin fractions.

The distribution of estradiol receptor and vitellogenin gene was studied in estradiol stimulated chick liver chromatin fractions prepared by limited DNAse II digestion and MgCl2 precipitation. The receptor was found in all fractions, undigested chromatin (P1), Mg2+ insoluble chromatin (P2) and Mg2+ soluble chromatin (S2). This last fraction was rich in acidic proteins, had a high protein:DNA ratio (7.0 w/w), contained 28% of rapidly labelled RNA, 20% of the receptor, 3-5% of chromatin DNA and showed a 2 fold enrichment of vitellogenin DNA sequences over unfractionated chromatin as well as P1 and P2 DNA. On isopycnic metrizamide gradients, all chromatin fractions showed a receptor peak banding at 1.23 g/cm3, the density of nucleoproteins. Hybridization experiments showed that the DNA banding at this density in fraction S2 was enriched 4 fold in vitellogenin DNA sequences over unfractionated chromatin as well as P1 and P2 DNA. These results suggest an association of hormone receptor complex with nucleoprotein structures of an apparently active chromatin fraction.     

The biosynthesis of nicotinamide adenine dinucleotide during early stages of frog embryonic development of haploid and diploid embryos.

1. Concentration of NAD during embryonic development of haploid and diploid embryos of frog was followed. NAD content in haploid embryonic forms is twice that in diploid embryos. 2. The variation of the NMN adenylyltransferase activity in the oocytes and during the first states of embryonic development as surveyed in the nuclear soluble fraction and the nuclear insoluble fraction (chromatin). 3. The enzyme activity in the soluble fraction is low during embryonic development and shows higher values in haploid embryos. 4. In the nonfertilized mature oocytes, the NMN adenylyltransferase activity is sixfold higher in the insoluble chromatin fraction than in the soluble fraction. 5. The evolution of the NMN adenylyltransferase in the insoluble chromatin fraction also shows higher values in haploid embryos, as compared with diploid forms.     

Proof of guanylate cyclase activity in the coronary artery of cattle]

Guanylate cyclase activities were identified in a soluble fraction and a particular fraction obtained from the Arteria coronaria of cattle. The Km-value was 1.0 +/- 0.7 - 10(-4) M for the enzyme substrate complex of the guanylate cyclase of the soluble fraction and 9.2 +/- 1.5 - 10(-4) M for the particular fraction. For the enzyme activity of the soluble fraction Mn++ cannot be replaced by Ca++ or Mg++, whereas for the enzyme activity of the particulate fraction Mn++ can be replaced by Mg++ but not by Ca++. The guanylate cyclase of the particulate fraction can be activated by acetylcholine. This activation can be cancelled by atropine. Acetylcholine exerts no influence on the guanylate cyclase activity of the soluble fraction. ATP inhibits the enzyme activities of both fractions whereas cAMP shows no influence on the guanylate cyclase activity.     

Demonstration of protein kinase activities in the coronary artery of cattle]

Protein kinase activities were identified in a soluble and a particulate fraction from the A. coronaria of cattle. For both protein kinase activities Mg++ is essential. Protamine was used as a substrate of the protein kinase activity of the soluble fraction. The pH optimum of the protein kinase activity of the soluble fraction is around 6.5. The Km-value of the protein kinase for ATP is 1.9 +/- 0.4 - 10(-5) M. cAMP stimulates the protein kinase activity more effectively than cGMP. Ca++ cannot replace Mg++; monovalent cations (Na+ and K+) show no influence. The protein kinase activity of the fraction was determined via endogenous phosphorylation. By means of the cAMP-dependent particulate protein kinase 72 to 80 percent of the serine residues are phosphorylated. The pH optimum of the protein kinase activity of the particulate fraction lies around 7.0. The Km-value of the enzyme for ATP is 6.6 +/- 0.8 - 10(-5) M. cGMP stimulates the protein kinase of the particulate fraction better than cAMP. For the protein kinase activity of this fraction Ca++ replaces Mg++ in the endogenous phosphorylation but not in the exogenous phosphorylation (protamine). In the presence of Mg++ and in the additional presence of Na+ or K+, the protein kinase activity is suppressed in the endogenous phosphorylation whereas it is stimulated in the exogenous phosphorylation.     

Sequence composition of the template-active fraction of rat liver chromatin.

Rat liver chromatin has been separated into nuclease-sensitive and -resistant fractions after mild digestion with DNAase II. The nuclease-sensitive material is further fractionated into Mg2+ -soluble and -insoluble chromatin fractions. The kinetics of production of these chromatin fractions have been investigated. After a brief enzyme treatment (5 min at 10 enzyme units/A260 unit of chromatin at pH 6.6), 11% of the input chromatin DNA is found in the Mg2+ -soluble fraction. This DNA has a weight-average single-strand length of about 400 nucleotides and, as determined by renaturation kinetics, comprises a subset of nonrepetitive DNA sequences and a subset of families of middle repetitive sequences. This demonstrates the nonrandom distribution of repetitive and single copy sequences in the Mg2+ -soluble fraction of chromatin. Previous studies have shown that the Mg2+ -soluble fraction is enriched in nonrepeated sequences which are transcribed in vivo (Gottesfeld, J.M., Garrard, W.T., Bagi, G., Wilson, R.F., and Bonner, J. (1974), Proc. Natl. Acad. Sci. U.S.A. 71, 2193-2197). We now report that the Mg2+ -soluble fraction of liver chromatin contains a low proportion of sequences in common with the Mg2+ -soluble fraction of brain chromatin. Thus, fractionation does not depend on some general property of chromatin but is specific with regard to the template activity of the tissue from which the chromatin was obtained.     

Polylysine titration of rat liver chromatin fractions after DNase II digestion.

The concentration of free phosphate groups is measured in rat liver chromatin after DNase II digestion using polylysine titration. The unsheared chromatin completely precipitates at lysine/DNA phosphate ratios of 0.5 to 0.6. Digestion of the chromatin reduces the lysine/DNA phosphate ratio of complete precipitation by about 0.2 units suggesting the removal of free phosphate groups. The two chromatin fractions: MgC12 insoluble (template-inactive) and Mg12 soluble (template-active) chromatins precipitate at about the same lysine/DNA phosphate ratio. Some 15% of the MgC12 soluble chromatin remains in solution at any polylysine concentration. The removal of histone H 1 FROM THE MgC12 insoluble chromatin increases the lysine/DNA phosphate ratio by about 0.2 units suggesting that 20% of the DNA phosphate groups in nucleosomes are masked by histone H 1.     

Potential role for 53BP1 in DNA end-joining repair through direct interaction with DNA

Upon DNA damage, p53-binding protein 1 (53BP1) relocalizes to sites of DNA double-strand breaks and forms discrete nuclear foci, suggesting its role in DNA damage responses. We show that 53BP1 changed its localization from the detergent soluble to insoluble fraction after treatment of cells with x-ray, but not with ultraviolet or hydroxyurea. Either DNase or phosphatase treatment of the insoluble fraction released 53BP1 into the soluble fraction, showing that 53BP1 binds to chromatin in a phosphorylation-dependent manner after X-irradiation of cells. 53BP1 was retained at discrete nuclear foci in X-irradiated cells even after detergent extraction of cells, showing that the chromatin binding of 53BP1 occurs at sites of DNA double-strand breaks. The minimal domain for focus formation was identified by immunofluorescence staining of cells ectopically expressed with 53BP1 deletion mutants. This domain consisted of conserved Tudor and Myb motifs. The Tudor plus Myb domain possessed chromatin binding activity in vivo and bound directly to both double-stranded and single-stranded DNA in vitro. This domain also stimulated end-joining by DNA ligase IV/Xrcc4, but not by T4 DNA ligase in vitro. We conclude that 53BP1 has the potential to participate directly in the repair of DNA double-strand breaks.     

Effect of potassium on uptake and incorporation of ammonium-nitrogen of rice plants

1. Rice was grown for 5 months in a sand solution culture at two different

1. K levels. The higher K supply resulted in a reduced uptake of Na +, Mg ++, and Ca++ by shoots. The uptake of NH4+-N of the shoots, however, was increased by the higher K supply.
2. In short term experiments, ill which the NH4+-N of the uptake solution was labelled by N 15, increasing K concentrations in the uptake solution did not depress the NH4 + uptake of young rice plants. Higher K concentrations in the uptake solution favoured the translocation of labelled N from the roots to the shoots. In some cases the higher K levels resulted also in an enhanced transfer rate of labelled N from the soluble to the insoluble N fraction.
3. Increasing levels of Mg++ in the uptake solution did not affect the uptake of labelled NH4-N.
4. I t is concluded that K + and NH4 + do not compete for common binding sites of the uptake mechanism in rice roots. This lacking competition suggests the speculation that NH4+-N is absorbed mainly in form of NH8 by plant cells.

     

Function of DNA Polymerase III in DNA Replication

RECENTLY an in vitro system for DNA replication has been described. This system could be divided into two fractions (A and B) both of which are necessary for proper DNA replication¹. Fraction A, the “soluble” fraction, contains those proteins which do not tightly bind to membranes or native DNA. Fraction B, the “insoluble” fraction, consists of DNA and membranous structures and proteins which are bound to either of them. It was shown that the soluble fraction contains at least one component which is needed at about in vivo concentration¹. Studies of one such component are described in the following.     

Condensation and precipitation of chromatin by multivalent cations

The condensation and the precipitation of rat liver chromatin upon addition of spermine4+, spermidine3+, hexamminecobalt(III)3+ and Mg2+ cations have been studied using solubility, fluorescence, circular dichroism, melting curves, electric dichroism and spermidine binding measurements, made on both soluble and precipitated complexes. The soluble complexes obtained with tetra- and trivalent cations were depleted from all histones and enriched in other proteins, particularly high mobility group proteins 1 and 2, which brings about an important enhancement of tryptophan fluorescence without modification of its two lifetimes 5.1 and 1.2 ns. In the precipitates the non-histone proteins are eliminated. Under precipitation by Mg2+ ions, the distribution of proteins remains practically unchanged. The electric dichroism and the melting curves indicate that the soluble complexes between polyamines and chromatin undergo important condensation and, at high ratios of cation over phosphate, are constituted by heterogeneous assemblies of non-histone proteins and DNA. On the contrary, the insoluble complexes seem to retain the main features of original chromatin. Precipitation by Mg2+ ions reveal much less drastic changes than those produced by polyamines. Precipitation by spermidine occurs when one cation is bound per eight nucleotides, which in addition to the histone positive charges brings about a complete neutralization of chromatin phosphates.     

Effect of chromatin decondensation on the intranuclear matrix

We have studied the effect of chromatin condensation on the morphology of the residual structures isolated from rat liver nuclei. DNAse I digestion followed by high salt extraction of nuclei in the presence of Mg++ yields residual structures consisting of a dense peripheral layer surrounding an internal network, similar to those described by Berezney and Coffey [6]. These structures are stable at low ionic strength in the presence of EDTA. When nuclei swollen in EDTA are digested with DNAse II in the presence of EDTA, structures devoid of internal network are obtained even without subsequent treatment with high salt. When swollen nuclei are exposed to Mg++ a specific recondensation of chromatin takes place. The residual structures from recondensed nuclei are similar to those isolated from control nuclei in the presence of Mg++. The results suggest that the integrity and stability of the intranuclear matrix are acquired in the course of the isolation procedure and this is favoured by chromatin condensation.     

Laser flow measurements of scattering and fluorescence from cell nuclei in the presence of increasing Mg++ concentrations.

The effects of Mg++ on the spatial organization of nuclei from rat hepatocytes are analyzed in the range 0-60 mM, in the presence of suitable concentrations of KCl to reproduce physiological conditions. It is shown that the scatter-signal distribution measured by means of a flow microfluorimeter is greatly affected by this range of Mg concentrations. By coupling this result to phase-contrast-automated image analysis, it is possible to identify a shrinking process induced by Mg++ in the range 0-2.5 mM, which reaches a plateau in the range 5-20 mM and is followed by a swelling process in the range 30-60 mM. The same Mg ranges are shown to affect the intercalation of the fluorochrome acridine orange into chromatin, suggesting that the shrinking-swelling phenomenon has also a molecular correspondence at the genome level. Possible implications in terms of the influence of Mg++ on the organization of chromatin inside intact cells are briefly discussed.     

Calmodulin and calmodulin-binding proteins in the renal brush border

The calmodulin content of renal brush-border membrane vesicles, prepared by Mg2+-precipitation in EGTA-containing solutions, amounts to 1.8 micrograms per mg protein. The amount and the distribution of this EGTA-insensitive calmodulin was determined in membrane and cytoskeletal fractions prepared from the brush-border membrane vesicles by extraction with Triton X-100. The Triton X-100 insoluble pellet contains 21.2% of the protein and 52.2% of the EGTA-insensitive calmodulin, which amounts in this fraction to 4.4 micrograms per mg protein. Treatment of the Triton X-100 insoluble pellet, consisting of the microvillar core residue, with ATP and Mg2+ results in the solubilization of a relatively small number of proteins among which are actin, myosin, calmodulin and several calmodulin-binding proteins. The solubilization is partially reversible and a fraction of the proteins can be precipitated by centrifugation after the enzymatic hydrolysis of ATP. Readdition of ATP to the pellet results in the resolubilization of myosin, part of the actin, an 115-kDa calmodulin-binding protein and calmodulin. The calmodulin content of the final extract was 61.8 micrograms per mg protein. We have found roughly the same distribution pattern of calmodulin and ATP-solubilized, calmodulin-binding proteins in renal and intestinal brush-border preparations. The calmodulin content, however, as well as the relative amount of the calmodulin-binding proteins versus actin are about 4 to 5-times higher in intestinal than in renal microvillar core residues.