ADP-ribosylation induced changes in the conformation of the chromatin of the brain of developing rats

Conformational changes in the chromatin of the cerebral hemisphere of 3-, 14- and 30-day old developing rats were studied before and after its ADP-ribosylation using DNase I and micrococcal nuclease (MNase). The rate and extent of digestion of chromatin by DNase I are the highest at 3-day and decline progressively thereafter. The rate and extent of digestion by MNase do not change during development. ADP-ribosylation of chromosomal proteins was carried out by incubating nuclei with NAD+ for 30 min and was followed by endonuclease digestion. Both the rate and extent of digestion by DNase I and MNase were enhanced after ADP-ribosylation which was the maximum for 3-day rats.     

Analysis of chromatin of the brain of young and old rats by micrococcal nuclease and DNase I

Micrococcal nuclease (MCN) and DNase I were used to study the conformational changes in chromatin of the brain of rats of different ages. Purified nuclei and chromatin were digested separately by MCN and DNase I. Kinetics of digestion of chromatin by MCN are similar for young, adult and old rats. Also agarose gel electrophoresis of DNA fragments do not show any differences. The kinetics of digestion with DNase I, on the other hand, are greater and faster for 20-week old rats than for 90-week old rats. High performance denaturing polyacrylamide gel electrophoresis reveals that a greater amount of smaller fragments of DNA are produced in the 20-week old rats than in the 90-week. These conformational changes occur in the chromatin during aging.     

Developmental changes in the chromatin of the brain of the rat: analysis by nicktranslation

Nick translation of nuclei of the brain of 3- 14- and 30-day old rats was carried out following their digestion by DNase I. The incorporation of ³H-dTMP at 14- and 30-day is significantly lower than at 3-day. This may be due to a lower proportion of active chromatin (DNase I hypersensitive sites) and condensation of chromatin with progressive development. When nuclei were digested by EcoRI and then nick-translated, the incorporation of ³H-dTMP showed the same pattern. Since the EcoRI sites are believed to be randomly distributed, the overall conformation of chromatin including the DNase I sensitive sites seems to undergo increasing compaction with development.     

Nucleosome positioning and periodicity of satellite DNA in the liver of aging rats – Nucleosome positioning and periodicity of satellite DNA

The positioning of nucleosomes has been analysed by comparing the pattern of cutting sites of a probing reagent on chromatin and naked DNA. For this purpose, high molecular weight DNA and nuclei from the liver of young (18±2 weeks) and old (100±5 weeks) Wistar male rats were digested with micrococcal nuclease (MNase) and hybridized with ³²P-labelled rat satellite DNA probe. A comparison of the ladder generated by MNase with chromatin and nuclei indicates long range organization of the satellite chromatin fiber with distinct non-random positioning of nucleosomes. However, the positioning of nucleosomes on satellite DNA does not vary with age. For studying the periodicity and subunit structure of satellite DNA, high molecular weight DNA from the liver of young and old rats were digested with different restriction enzymes. Surprisingly, no noteworthy age-related change is visible in the periodicity and subunit structural organization of the satellite DNA. These results suggest that the nucleosome positioning and the periodicity of liver satellite DNA do not vary with age.     

Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin

We have used line HS-2 of Drosophila melanogaster, carrying a silenced transgene in the pericentric heterochromatin, to investigate in detail the chromatin structure imposed by this environment. Digestion of the chromatin with micrococcal nuclease (MNase) shows a nucleosome array with extensive long-range order, indicating regular spacing, and with well-defined MNase cleavage fragments, indicating a smaller MNase target in the linker region. The repeating unit is ca. 10 bp larger than that observed for bulk Drosophila chromatin. The silenced transgene shows both a loss of DNase I-hypersensitive sites and decreased sensitivity to DNase I digestion within an array of nucleosomes lacking such sites; within such an array, sensitivity to digestion by MNase is unchanged. The ordered nucleosome array extends across the regulatory region of the transgene, a shift that could explain the loss of transgene expression in heterochromatin. Highly regular nucleosome arrays are observed over several endogenous heterochromatic sequences, indicating that this is a general feature of heterochromatin. However, genes normally active within heterochromatin (rolled and light) do not show this pattern, suggesting that the altered chromatin structure observed is associated with regions that are silent, rather than being a property of the domain as a whole. The results indicate that long-range nucleosomal ordering is linked with the heterochromatic packaging that imposes gene silencing.     

Calcium protects DNase I from proteinase K: a new method for the removal of contaminating RNase from DNase I

DNase I and proteinase K are two enzymes commonly used in the purification of highly polymerized RNA. In the presence of EDTA DNase I is rapidly inactivated by proteinase K while in 10 mm Ca²⁺ DNase is totally immune to proteinase K inactivation even at protease concentrations of up to 1 mg/ml. RNase A, a common contaminant of “RNase-free” DNase was inactivated by proteinase K in the presence or absence of Ca²⁺. Treatment of DNase I with proteinase K in the presence of Ca²⁺ selectively removed RNase A activity as judged by rRNA and poly(A⁺ RNA ribosomal RNA degradation monitored by sucrose gradient centrifugation. These results suggest that (i) DNase A and proteinase K can be used together in the presence of Ca²⁺ to obtain better digestion of nucleoprotein complexes, and (ii) proteinase K treatment of Ca²⁺ DNase can be used to selectively remove contaminating RNase.     

Conformational changes in the chromatin of the brain of developing rats and its modulation by zinc chloride

Conformational changes in the chromatin of the brain were studied during the development of the rat (3-, 14-and 30-day old) using microccoccal nuclease (MCN) and DNase I. The rate and extent of digestion of chromatin by MCN is not altered during development. However, pre-incubation of slices of the cerebral cortex with ZnCl₂ increases the initial rate of digestion by MCN by 2–3-fold, and also enhances the production of monomer DNA. The rate and extent of digestion of chromatin by DNase I is greater in an early stage of development. The initial rate of digestion by DNase I is stimulated by 3–4-fold after ZnCl₂ treatment. These data show that changes occur in the conformation of chromatin, particularly in the internucleosomal region of brain cells as they pass from dividing to the non-dividing state.     

Passive Ca binding in ventricular myocardium of neonatal and adult rats

In this study, passive Ca²⁺ binding was determined in ventricular homogenates (VH) from neonatal (4–6 days) and adult rats, as well as in digitonin-permeabilized adult ventricular myocytes. Ca²⁺ binding sites, both endogenous and exogenous (Indo-1 and BAPTA) were titrated. Sarcoplasmic reticulum and mitochondrial Ca²⁺ uptake were blocked by thapsigargin and Ru360, respectively. Free [Ca²⁺] ([Ca²⁺]_F was measured with Indo-1 and bound Ca²⁺ ([Ca²⁺]_B) was the difference between [Ca²⁺]_F and total Ca²⁺. Apparent Ca²⁺ dissociation constants (K_d) for BAPTA and Indo-1 were increased by 10–20 mg VH protein/ml (from 0.35 to 0.92 μM for Indo-1 and from 0.20 to 0.76 μM for BAPTA) and also by ruthenium red in the case of Indo-1. Titration with successive CaCl₂ additions (2.5–10 nmoles) yielded δ[Ca²⁺]_B/δ[Ca²⁺]_F for the sum of [Ca²⁺]_B at all three classes of binding sites. From this function, the apparent number of endogenous sites (B_en) and their K_d (K_en) were determined. Similar K_en values were obtained in neonatal and adult VH, as well as in adult myocytes (0.68 ± 0.14 μM, 0.69 ± 0.13 μM and 0.53 ± 0.10 μM, respectively). However, B_en was significantly higher in adult myocytes than in adult VH (1.73 ± 0.35 versus 0.70 ± 0.12 nmol/mg protein, P < 0.01), which correspond to ∼300 and 213 μmol/l cytosol. This indicates that binding sites are more concentrated in myocytes than in other ventricular components and that B_en determined in VH underestimates cellular B_en by 29%. Although B_en values in nmol/mg protein were similar in adult and neonatal VH (0.69 ± 0.12), protein content was much higher in adult ventricle (125 ± 7 versus 80 ± 1 mg protein/g wet weight, P < 0.01). Expressing B_en per unit cell volume (accounting for fractional mitochondrial volume, and 29% dilution in homogenate), the passive Ca²⁺ binding capacity at high-affinity sites is ∼300 and 176 mmol/I cytosol in adult and neonatal rat ventricular myocytes, respectively. Additional estimates suggest that passive Ca²⁺ buffering capacity in rat ventricle increases markedly during the first two weeks of life and that adult levels are attained by the end of the first month.     

Effects of Calcium on Template Activity and Size of Pea Chromatin Fragments

Pea chromatin was fractionated into template active and inactivefragments by cleavage with DNase II followed by fractionationwith Bio-Gel A 5 m column chromatography. When the chromatin fragments were chromatographed in the presenceof Ca²⁺ or EGTA, the elution patterns suggested that Ca²⁺ assembledmoderately digested chromatin fractions. Moreover, total templateactivity of chromatin fractions was reduced by Ca²⁺ and theactive fraction was eluted at different positions under thechelated and non-chelated conditions. (Received February 12, 1986; Accepted May 28, 1986)     

Androgen treatment protects mouse liver chromatin from cleavage by endogenous nucleases during aging

We have examined the endogenous nuclease activity of the liver of intact, castrated and testosterone-treated mice of different ages. Both Mg²⁺- and Ca²⁺-dependent endogenous nuclease activities decline in old age. Withdrawal of the hormone increases nuclease activity in the immature and young. However, testosterone administration prevents the digestion of nuclei to different extents in all ages. These findings suggest a possible protective role of testosterone in the cleavage of liver chromatin by endogenous nucleases during the aging of mice.     

The mechanism and pattern of banding induced by restriction endonucleases in human chromosomes

The mechanism of chromosome banding induced by restriction endonucleases was analyzed by measuring the amount of radioactivity extracted from [¹⁴C]thymidine-labeled chromosomes digested first with restriction enzymes and subsequently with proteinase K and DNase I. Restriction enzymes with a high frequency of recognition sites in the DNA produced a large number of short DNA fragments, which were extracted from chromosomes during incubation with the enzyme. This loss of DNA resulted in decreased chromosomal staining, which did not occur in regions resistant to restriction enzyme digestion and thus led to banding. Subsequent digestion of chromosomes with proteinase K produced a further loss of DNA, which probably corresponded to long fragments retained in the chromosome by the proteins of fixed chromatin. Restriction enzymes induce chromatin digestion and banding in G1 and metaphase chromosomes, and they induce digestion and the appearance of chromocenters in interphase nuclei. This suggests that the spatial organization and folding of the chromatin fibril plays little or no role in the mechanism of chromosome banding.It was confirmed that the pattern of chromosome banding induced by AluI, MboI, HaeIII, DdeI, RsaI, and HinfI is characteristic for each endonuclease. Moreover, several restriction banding polymorphisms that were not found by conventional C-banding were detected, indicating that there may be a range of variability in the frequency and distribution of restriction sites in homologous chromosome regions.     

Estrogen induces tissue specific changes in the chromatin conformation of the vitellogenin genes in Xenopus.

Nuclei from male Xenopus liver were digested extensively with DNase I and the residual amount of the four vitellogenin genes measured by hybridization with a moderate excess of vitellogenin cDNA. The saturation value was about twofold lower in chromatin isolated from liver cells of estrogen treated than from untreated males or from erythrocytes. Analyzing the disappearance of several defined restriction fragments specific for the A1 and A2 vitellogenin genes, after limited digestion with DNase I, suggested that the entire A1 and A2 vitellogenin genes are about twofold more sensitive to DNase I in chromatin of hepatocytes isolated from estrogen treated than from untreated males. Using the same assay no change in the DNase I sensitivity of the two vitellogenin genes in erythrocyte chromatin was observed. Analysis of the beta 1-globin and an albumin gene demonstrated that the DNase I sensitivity of these genes in both cell types is not altered by estrogen. All these data indicate that estrogen stimulation results in an increased DNase I sensitivity specific for the vitellogenin genes in hepatocytes.     

Chromatin regions,released by endogenous nucleases,are enriched in immunogenic tissue-specific proteins

Localization of immunogenic tissue-specific proteins in chromatin regions, hypersensitive to endogenous nucleases, has been studied using rabbit antibodies against rat thymus chromatin. It is shown that the first 1–2,5% of the chromatin (calculating on DNA), released by Mg²⁺-, Mn²⁺-, and Ca²⁺/Mg²⁺-dependent nuclear endonucleases are drastically enriched in tissue-specific antigenic determinants. The released chromatin fractions are found to contain a heterogeneous set of nonhistone proteins and are deficient in histones. The cleavage of nuclear DNA by endogenous acidic nuclease, independent on bivalent ions, resulted in a significantly less enrichment of the released fractions with immunogenic proteins.