Rat Liver Chromatin Research Articles

Melting calorimetry of rat liver nuclei in the presence of magnesium ions

Differential scanning calorimetry was used to determine thermodynamic parameters of decondensation of intranuclear rat liver chromatin was induced by a decrease in the concentration of magnesium ions from 5 mM to 0 mM. The process of chromatin melting in the temperature range of 70-100°C occurs in the following order: melting of core-histones, melting of relaxed DNA, and melting of topologically constrained DNA. It was found that Tm and Д H of individual peaks also depend on the concentration of Mg2+ ions in the buffer. In nuclei with condensed chromatin, Mg2+ ions at a concentration of 5 mM increased significantly the Tm of core histones (by ~7°C), as compared to that in unfolded chromatin but at the same time lowered the Tm of nuclear DNA both in the relaxed and constrained state (by ~2.5°С and ~7.5°С, respectively). In the presence of Mg2+ ions, melting enthalpy for peaks increased significantly. At the same time, a decrease in molecular weights of intranuclear DNA levels out a stabilizing effect of Mg2+ ions on core histones. A rise in the concentration of Mg2+ ions above 5 mM leads to the appearance of a new peak with Tm above 100°С, which probably reflects the thermal behavior of some Mg-induced aggregates. Possible mechanisms underlying thermal behavior of chromatin inside the nucleus are discussed.

Investigation on the chromium oxide interaction with soluble chromatin and histone H1: A spectroscopic study

Chromatin has been introduced as a tool for studying heavy metals action in nuclei. Chromium oxide is highly soluble and toxic with chronic exposure leading to mutagenesis and carcinogenesis. In the present study, for the first time, the binding affinity of chromium oxide to rat liver chromatin and histone proteins was investigated. Reduction of chromatin absorbencies at 210 and 260nm (hypochromicity) and fluorescence emission intensity upon metal binding represented quenching of the metal with chromatin chromophores. Binding isotherms demonstrated a positive cooperative binding pattern revealing higher affinity of the metal to chromatin compared to DNA as confirmed by the binding constants. Melting temperature of chromatin was altered in a dose dependent manner and suggests partial removal of histones from the chromatin at metal concentrations higher than 15μg/ml. Chromium oxide decreased the absorbance of histone H1 at 210nm (hypochromicity) and fluorescence emission intensity revealed quenching of the metal with tyrosine residue located in the core domain of H1. Also the interaction of chromium oxide with histone H1 increased its secondary structures. The results suggest toxic effect of very low concentrations of chromium oxide on chromatin and in this reaction both DNA and histones are involved.

Toxic effects of lead and nickel nitrate on rat liver chromatin components

The biological activity of heavy metals is related to their physicochemical interaction with biological receptors. In the present study, the effect of low concentrations of nickel nitrate and lead nitrate (<0.3 mM) on rat liver soluble chromatin and histone proteins was examined. The results showed that addition of various concentrations of metals to chromatin solution preceded the chromatin into aggregation and precipitation in a dose-dependant manner; however, the extent of absorbance changes at 260 and 400 nm was different between two metals. Gel electrophoresis of histone proteins and DNA of the supernatants obtained from the metal-treated chromatin and the controls revealed higher affinity of lead nitrate to chromatin compared to nickel nitrate. Also, the binding affinity of lead nitrate to histone proteins free in solution was higher than nickel. On the basis of the results, it is concluded that lead reacts with chromatin components even at very low concentrations and induce chromatin aggregation through histone-DNA cross-links. Whereas, nickel nitrate is less effective on chromatin at low concentrations, suggesting higher toxicity of lead nitrate on chromatin compared to nickel.

Dispersed Chromosomal Stat5b-binding Elements Mediate Growth Hormone-activated Insulin-like Growth Factor-I Gene Transcription

The growth hormone (GH)-insulin-like growth factor-I (IGF-I) axis regulates somatic growth during childhood and orchestrates tissue repair throughout the life span. Recently described inactivating mutations in Stat5b in humans with impaired growth have focused attention on this transcription factor as a key agent linking GH-stimulated signals to IGF-I gene expression, and several putative Stat5b sites have been identified in the IGF-I gene. Here, we define and characterize potential GH- and Stat5b-activated chromosomal enhancers that can regulate IGF-I gene transcription. Of 89 recognizable Stat5 sequences in 200 kb centering on the rat IGF-I gene, 22 resided within conserved regions and/or were identical among different species. Only 15 of these sites, organized into 7 distinct domains, were found to bind Stat5b by quantitative chromatin immunoprecipitation assays in liver chromatin of rats, but only after acute GH treatment. These sites could bind Stat5b in vitro, and individual domains could mediate GH- and Stat5b-stimulated IGF-I promoter activity in cultured cells. Further analyses revealed that four Stat5b domains possessed chromatin signatures of enhancers, including binding of co-activators p300 and Med1, and RNA polymerase II. These modifications preceded GH-stimulated recruitment of Stat5b, as did lysine 4 monomethylation of histone H3, which was enriched in 6/7 Stat5b-binding elements. In contrast, histone acetylation was induced by GH but was limited to Stat5b binding domains found within the IGF-I transcription unit. We conclude that GH stimulates recruitment of Stat5b to multiple dispersed regions within the igf1 locus, including several with properties consistent with long range transcriptional enhancers that collectively regulate GH-activated IGF-I gene transcription.

Alteration of the structure and function of rat liver chromatin by nutritional factors.

Alteration of the structure and function of rat liver chromatin by nutritional factors.

A comparison of the effect of lead nitrate on rat liver chromatin, DNA and histone proteins in solution

Although lead is widely recognized as a toxic substance in the environment and directly damage DNA, no studies are available on lead interaction with chromatin and histone proteins. In this work, we have examined the effect of lead nitrate on EDTA-soluble chromatin (SE chromatin), DNA and histones in solution using absorption and fluorescence spectroscopy, thermal denaturation and gel electrophoresis techniques. The results demonstrate that lead nitrate binds with higher affinity to chromatin than to DNA and produces an insoluble complex as monitored at 400 nm. Binding of lead to DNA decreases its Tm, increases its fluorescence intensity and exhibits hypochromicity at 210 nm which reveal that both DNA bases and the backbone participate in the lead-DNA interaction. Lead also binds strongly to histone proteins in the absence of DNA. The results suggest that although lead destabilizes DNA structure, in the chromatin, the binding of lead introduces some sort of compaction and aggregation, and the histone proteins play a key role in this aspect. This chromatin condensation, upon lead exposure, in turn may decrease fidelity of DNA, and inhibits DNA and RNA synthesis, the process that introduces lead toxicity at the chromatin level.

Thematic Review Series: Sphingolipids. Nuclear sphingolipids: metabolism and signaling

Sphingolipids are most prominently expressed in the plasma membrane, but recent studies have pointed to important signaling and regulatory roles in the nucleus. The most abundant nuclear sphingolipid is sphingomyelin (SM), which occurs in the nuclear envelope (NE) as well as intranuclear sites. The major metabolic product of SM is ceramide, which is generated by nuclear sphingomyelinase and triggers apoptosis and other metabolic changes. Ceramide is further hydrolyzed to free fatty acid and sphingosine, the latter undergoing conversion to sphingosine phosphate by action of a specific nuclear kinase. Gangliosides are another type of sphingolipid found in the nucleus, members of the a-series of gangliotetraose gangliosides (GM1, GD1a) occurring in the NE and endonuclear compartments. GM1 in the inner membrane of the NE is tightly associated with a Na(+)/Ca(2+) exchanger whose activity it potentiates, thereby contributing to regulation of Ca(2+) homeostasis in the nucleus. This was shown to exert a cytoprotective role as absence or inactivation of this nuclear complex rendered cells vulnerable to apoptosis. This was demonstrated in the greatly enhanced kainite-induced seizure activity in knockout mice lacking gangliotetraose gangliosides. The pathology included apoptotic destruction of neurons in the CA3 region of the hippocampus. Ca(2+) homeostasis was restored in these animals with LIGA-20, a membrane-permeant derivative of GM1 that entered the NE and activated the nuclear Na(+)/Ca(2+) exchanger. Some evidence suggests the presence of uncharged glycosphingolipids in the nucleus.

Arachidonic acid hydroperoxide stimulates lipid peroxidation in rat liver nuclei and chromatin fractions

Arachidonic acid, the most abundant polyunsaturated fatty acid in rat liver nuclei phospholipids is a major target of free radical attack, which induces lipid peroxidation. The non-enzymatic lipid peroxidation process in intact rat liver nuclei and in several chromatin fractions indicated that the most sensitive fatty acid for peroxidation is arachidonic acid C20:4 n-6. In this study, the effect of different amounts of arachidonic acid hydroperoxide on the lipid peroxidation of rat liver nuclei and chromatin fractions was studied; rat liver nuclei and chromatin fractions deprived of exogenous added hydroperoxide were utilized as control. The addition of arachidonic acid hydroperoxide to liver nuclei produces a marked increase in light emission that was hydroperoxide concentration dependent. The maximal peak of chemiluminescence displayed by the different chromatin fractions analyzed was observed between 20 and 80 min of incubation. The highest value of light emission was displayed by the high-density chromatin fractions, the 27.5 K fraction showed intermediate values of light emission, whereas the lowest density fraction produced very low chemiluminescence. A high correlation between arachidonic acid hydroperoxide concentration and chemiluminescence in the different chromatin fractions was observed.

Changes in Composition of Acid Soluble Proteins and DNA in Chromatin of Rat Liver and Brain Bound and Not Bound to Nuclear Envelope as a Function of Age and under the Influence of Antioxidant Ionol

In two-day rat pups, the histone H1 content in the brain chromatin was higher than in the liver chromatin, as compared to histone of the nucleosome core. The H1 content in the brain chromatin decreased with the age, while in the liver chromatin it increased. At the same time, in the adult brain chromatin bound to the nuclear envelope, a high level of H1 characteristic of chromatin of the newborn rats was preserved, while in a similar chromatin of the adult liver, the H1 content increased, but still remained less than in the chromatin not bound to the nuclear envelope. In both organs, the composition and quantitation of H1 subfractions were different in chromatins bound and not bound to the nuclear envelope. The chromatin from the liver and brain bound to the nuclear envelope differed also in the composition and quantitation of minor acid soluble proteins. In the presence of the antioxidant ionol, the 5-methylcytosine content in DNA of chromatin of the rat liver bound to the nuclear envelope increased while in the chromatin not bound to the nuclear envelope, it remained unchanged. Thus the chromatins bound and not bound to the nuclear envelope differ in the composition and mount of acid soluble proteins, including histone H1, the contents of these proteins in bound and not bound chromatin are different and change with the age in different ways. The antioxidant ionol affects differently the methylation of bound and not bound chromatin.

Excision of apurinic sites from DNA with enzymes isolated from rat-liver chromatin.

Apurinic sites were excised from phi X174 RF DNA with two enzymes isolated from rat liver chromatin: an apurinic/apyrimidinic endodeoxyribonuclease and a 5'-3'-exonuclease; the resulting gap was filled with DNA polymerase beta also prepared from rat liver chromatin and the repair was fully terminated with T4 ligase.

Binding of (MTR) 2Zn 2+ complex to chromatin: a comparison with (MTR) 2Mg 2+ complex

Mithramycin (MTR), a member of aureolic group of anticancer antibiotic, binds reversibly to double stranded DNA via minor groove with (G.C) base specificity. It leads to inhibition of replication and transcription. Results from different laboratories have shown that at and above physiological pH, Mg 2+ is an obligatory factor for the DNA binding and subsequent transcription inhibitory property of mithramycin. Zn 2+ is another physiologically important bivalent cation. Its coordination property leads to its important role as a cofactor in different enzymes and nucleosomal DNA binding proteins. Characterization of the complex between mithramycin and Zn 2+ using spectroscopic methods shows that the drug forms single type of complex with Zn 2+ in the mole ratio of 2:1 in terms of antibiotic: Zn 2+. DNA binding properties of the (MTR) 2Zn 2+ complex has been studied using calf thymus DNA, rat liver chromatin and nucleosome core. (MTR) 2Zn 2+ complex binds to calf thymus DNA with affinity higher than the corresponding dimer complex with Mg 2+ ion. The presence of histone proteins in chromatin and nucleosome reduces the accessibility and hence binding potential of (MTR) 2Zn 2+ complex to nucleosomal DNA. We have also examined the effect of (MTR) 2Zn 2+ complex upon the stability of nucleosome core particle. The complex disassembles nucleosome structure leading to the release of nucleosomal DNA. Significance of the results to understand the molecular basis of the action of the drug in vivo is discussed.

Polynucleosomal Synthesis of Poly(ADP‐ribose) Causes Chromatin Unfolding as Determined by Micrococcal Nuclease Digestion

We have evaluated the influence of protein poly(ADP-ribosyl)ation in the relaxation of chromatin by exposing a rat liver polynucleosomal extract to micrococcal nuclease (MNase) digestion. The kinetic susceptibility of polynucleosomes to endonuclease digestion was determined as a function of the time of incubation as well as endonuclease concentration. To validate our assay, we also ran control experiments with protein-free calf thymus DNA as the opposite of polynucleosomal DNA. Rat liver chromatin was also incubated in the absence or presence of exogenously added 200 microM betaNAD(+), the poly(ADP-ribosyl)ation substrate, before MNase digestion. For incubations in the presence of betaNAD(+), the synthesis of polynucleosomal poly(ADP-ribose) was stopped with 1 mM benzamide. After addition of MNase, endonuclease digestion was blocked with EDTA to chelate the Mg(2+) ions needed for enzymatic activation, and the samples were subjected to electrophoresis through 1.5% agarose gels. As expected, a faster degradation of chromatin into oligonucleosomal DNA ladders was observed upon protein poly(ADP-ribosyl)ation when the chromatin extract was preincubated with 200 microM betaNAD(+). Thus, our results are consistent with the conclusion that the covalent poly(ADP-ribosyl)ation of polynucleosomal proteins favors a more "relaxed" or "open" structure, which renders chromatin more susceptible to MNase digestion.

Plasmalogens in rat liver chromatin: new molecules involved in cell proliferation.

A minor component of chromatin, the phospholipid fraction, changes during cell cycle as result of the activation of intranuclear lipid metabolism enzymes including phosphatidylcholine-dependent phospholipase C activity. It is known that this enzyme may be activated by phosphatidylcholine plasmalogen (Plg). Until now, there has been little evidences for the presence of Plgs inside the nucleus. The aim of our study is to ascertain if they are present in the nucleus and are responsible of the activation of phosphatidylcholine-dependent phospholipase C during cell proliferation and apoptosis. Therefore, we have analysed the Plg composition of the whole homogenate, cytosol, nuclei and chromatin of hepatocytes. The phosphatidylcholine-dependent phospholipase C activity was assayed using both phosphatidylcholine and plasmalogenyl-phosphatidylcholine as substrates. Our results show, for the first time, that Plgs are present in chromatin and the plasmalogenyl-phosphatidylcholine stimulates the phosphatidylcholine-dependent phospholipase C activity more than phosphatidylcholine. Finally, in order to verify the possible role of these molecules during cell proliferation and apoptosis, we used liver of rats fed with ciprofibrate which stimulates hepatocytes proliferation during the treatment and, after withdrawal, apoptosis. After 3 days of ciprofibrate treatment, the chromatin plasmalogenyl-phosphatidylcholine increases as well as the phosphatidylcholine-dependent phospholipase C activity. After drug withdrawal, when the hepatocytes undergo to apoptosis, the plasmalogenyl-phosphatidylcholine content together with phosphatidylcholine-dependent phospholipase C activity decreases. Therefore, it can be concluded that plamalogens are present in the chromatin, and probably may have a function both in regulating phosphatidylcholine dependent phospholipase C and cell cycle.

Association of chromatin with anticancer antibiotics, mithramycin and chromomycin A3

Mithramycin and chromomycin A3 are two anticancer antibiotics, which inhibit protein biosynthesis via transcription inhibition. They bind reversibly to DNA with (G.C) base specificity. At and above physiological pH in the absence of DNA, they form two types of complexes with Mg2+, complex I (1:1 in terms of antibiotic: Mg2+) and complex II (2:1 in terms of antibiotic: Mg2+). These are the DNA binding ligands. In vivo, the antibiotics interact with chromatin, a protein–DNA complex. In order to understand the mode of action of these antibiotics at molecular level, we have carried out spectroscopic, gel electrophoretic and UV melting studies of complex I of these antibiotics with rat liver chromatin, nucleosome core particle and DNA stripped of all chromosomal proteins. Analysis of the results has led us to propose that the antibiotic: Mg2+ complex binds to both nucleosomal and linker DNA in native chromatin. Histone proteins reduce the binding potential and accessibility of the complexes to the minor groove of (G.C) rich regions of chromosomal DNA. The antibiotic: Mg2+ complex stabilizes DNA duplex and histone- DNA contacts in chromatin fiber. It also leads to the aggregation of chromatin fibers. From a comparison of the association of the antibiotic: Mg2+ complexes with different levels of chromatin structure and their effects upon the structure, we suggest that the sugar moieties of the antibiotics play a role in the binding process. Significance of these results to understand the molecular basis of the transcription inhibition potential of the antibiotics in eukaryotes is discussed.

Interaction of a low mobility group protein, LMG 160, with deoxyribonucleic acid

A fraction of low mobility group (LMG) nonhistone protein designated LMG 160 was isolated from rat liver chromatin by preparative gel electrophoresis and its interaction with DNA was studied using thermal denaturation and DNA–cellulose affinity chromatography techniques. The results showed that LMG 160 with an isoelecteric point of 5–5.5 was bound to DNA and decreased its melting temperature. Increasing ionic strengths decreased this effect. DNA–cellulose affinity chromatography showed the affinity of LMG 160 to double stranded DNA was higher than that to single stranded DNA, since it required 0.6 M NaCl for elution. The results suggest that LMG 160 protein preferentially binds to double stranded DNA destabilizes it and the binding is electrostatic.

Nuclear and chromatin lipids: metabolism in normal and γ-irradiated rats

The data on nuclear and chromatin lipid metabolism are reviewed. The amount of neutral lipids and phospholipids in nuclei of rat thymus, liver and neocortex neuron as well as the amount of lipids in rat thymus and liver chromatin are described. The metabolic responses of nuclear and chromatin lipids from thymus to different doses and dose rates of γ-irradiation of rats are discussed. In most cases, the nuclear and chromatin lipid responses are distinct. Changes in nuclear and chromatin lipid metabolism in response to γ-irradiation are suggested to connect with the signal transduction pathway and the regulation of the transcriptional and replicative chromatin activity. The influence of β-carotene and picrotoxin on rat liver nuclear lipids and neocortex neuronal nuclear lipids, respectively, was analyzed. The possible involvement of the lipid traffic in the chromatin lipid responses to γ-irradiation and other agents is suggested.

Differences in the nuclear chromatin among various stages of the life cycle of Trypanosoma cruzi.

Trypanosoma cruzi is the etiological agent of Chagas. Although the nuclear chromatin of this parasite is organized in the form of nucleosome filaments, its chromatin is physically and enzymatically fragile, and no condensation into chromosomes occurs during mitosis. All previous investigations have been carried out with epimastigote form in its proliferate stage. It is not known whether these differences in chromatin structure are also found in the non-proliferate stationary epimastigote forms and in tissue derived trypomastigotes. Our results confirm that chromatin of logarithmic epimastigotes presents limited compaction when increasing salt concentrations from 1 to 100 mM NaCl, and no 30-nm fibers were formed. Contrary to these results, non-proliferative forms of the parasites showed a pattern of compactation similar to that observed in rat liver chromatin, where solenoids of 30-nm fibers are formed at 100-mM NaCl. In accordance with these results, digestion of the nuclear chromatin with DNase I revealed that the chromatin of logarithmic phase epimastigotes was more accessible to the enzyme. We conclude from these results that structural differences in the chromatin exist not only between T. cruzi and higher eukaryotes but also among various forms of the parasite. The functional significance of these differences are currently under investigation.

Incorporation of 1- 14C linoleic acid in rat liver nuclei and chromatin fractions

The incorporation of 1- 14C linoleic acid in several chromatin fractions of rat liver nuclei was investigated using two different procedures: (1) rat liver nuclei were incubated with ATP, CoASH, Mg ++ and 1- 14C linoleic acid. After 40 min at 37°C the chromatin obtained by sonication of nuclei suspended in 0.25 M sucrose was fractionated by differential sedimentation; (2) chromatin fractions obtained by differential sedimentation were incubated separately with ATP, CoASH, Mg ++ and 1- 14C linoleic acid 40 min at 37°C in order to characterize the fatty acid incorporation in isolated chromatin. A comparative study of the incorporation of 1- 14C linoleic acid in microsomes and nuclei isolated from rat liver is also presented for the purpose of comparison. Linoleic acid was incorporated into nuclear lipids as well as in chromatin fractions. The fatty acid incorporation was stimulated considerably in the acylation system when compared to control, it appears to be highly dependent on the state of condensation of chromatin, being barely detectable in the lowest density fraction. The major proportion of 1- 14C linoleic acid was found in phospholipids and in a lesser proportion it remained esterified to triglycerides and cholesteryl esters. The distribution of radioactivity in different classes of phospholipids present in microsomes and nuclei isolated from rat liver, showed a similar profile of distribution. The major proportion of radioactivity, approximately 50% was found in phosphatidylcholine and in a lesser proportion in sphingomyelin, phosphatidylserine and phosphatidylethanolamine. When chromatin fractions were incubated separately, it was observed that the major proportion of 1- 14C linoleic acid in phospholipids was found in heavy chromatin fractions whereas low density chromatin fraction only incorporated in a lesser proportion.

Sphingomyelin synthase in rat liver nuclear membrane and chromatin

The presence of phospholipids in chromatin has been demonstrated, as well as the difference in composition and turnover compared to those present in the nuclear membrane. Recently, some enzymes were also evidenced in chromatin: the base exchange protein complex and neutral sphingomyelinase. The latter has a particular relevance, since sphingomyelin is one of the phospholipids more represented in chromatin. We therefore decided to study the synthesis of sphingomyelin in chromatin and in nuclear membrane isolated from liver nuclei. The evaluation of the enzyme was made (i) using [ 3H]phosphatidylcholine as donor of radioactive phosphorylcholine and (ii) by identifying the product isolated by thin layer chromatography. In both fractions the enzyme phosphatidylcholine:ceramide phosphocholine transferase or sphingomyelin synthase was present, although with higher activity in nuclear membrane. The enzyme present in the chromatin differs in pH optimum and K m, showing a higher affinity for the substrates than that of nuclear membrane. The results presented show that sphingomyelin synthase is present not only in the cytoplasm at the level of the Golgi apparatus, but also in the nuclei, at the level of either the nuclear membrane or the chromatin.

Non-enzymatic lipid peroxidation of rat liver nuclei and chromatin fractions

In the study reported here, the non-enzymatic (ascorbate–Fe 2+) lipid peroxidation of rat liver nuclei and chromatin fractions was assayed. Chromatin obtained by sonication of nuclei suspended in 0.25 M sucrose was fractionated by differential sedimentation according to the following scheme: 3000, 12000 and 27500 g for 10 min each. The lowest density chromatin fraction was obtained by precipitation with cold ethanol of the supernatant obtained from the last centrifugation. Light emission=chemiluminescence, measured as cpm/mg protein, decreased in the order heavy>low density chromatin fractions during the peroxidation process. Analysis of fatty acids by gas chromatography showed that heavy density chromatin fractions are enriched with C20:4 n6 arachidonic acid, when compared with low density chromatin fractions. The amount of arachidonic acid C20:4 n6 was higher in repressed chromatin fractions as compared to the amount in the transcriptionally active chromatin which correlates with the level of lipid peroxidation.