Effect of Calcium on the Structure and Template Activity of Pea Chromatin

The absorption spectrum of native pea chromatin solubilizedunder minimal shearing conditions changed with increasing Ca²⁺concentration; the ratio of maximum to minimum absorption decreasedand the maximum absorption peak shifted to a longer wavelength.The concentration of Ca²⁺ to cause half complete sedimentationof chromatin was much lower for the solubilized native chromatin(more condensed and larger in size) than for the sonicated chromatin(less condensed and smaller in size). Solubilized native chromatinshowed a two-step melting profile in the absence of Ca²⁺. In the presence of Ca²⁺ the two T_ms disappeared and a new higherT_m appeared. Template activity of solubilized native chromatinincreased 3-fold upon dispersion and fragmentation by sonication.Addition of a small amount of ethylene glycol-bis (ß-aminoethylether)-N, N'-tetraacetic acid (EGTA) promoted the template activityof solubilized native chromatin, but not that of sonicated ordenatured DNA. The effect of EGTA was reversed by Ca²⁺. Thechromatin reconstituted in the presence of EGTA showed a lowerT_m than the chromatin reconstituted in the presence of Ca²⁺.The relationship between chromatin structure and its templateactivity is discussed in relation to Ca²⁺. (Received August 12, 1985; Accepted December 7, 1985)     

The nature of N-, P- and K-deficiency effects in rice

Effects of N-, P- and K-deficiencies on RNA synthesis in TN-1rice, Sonalika wheat and B-75 gram was examined at the molecularlevel. The melting temperatures of the chromatin of TN-1 rice,Sonalika wheat and B-75 gram was increased by deficiency conditions.In TN-1 rice the template activity of chromatin was reducedconsiderably, most remarkably in the case of the N-deficiency.The base composition of the newly synthesized RNA of the deficientroots also was altered. These changes were accompanied by anincrease in the histone-DNA ratio. There was, however, no qualitativechange in the histone patterns. The chromatin of deficient tissuesbound less actinomycin D than did that of the control, and thebinding of labelled cations and anions also decreased. In deficientplants endo- and exo-nuclease activities were enhanced, accompaniedby decreases in the intrinsic viscosity, sedimentation co-efficientand chain lengths of DNA. ¹This work was supported by a grant from the Department of AtmicEnergy, Government of India. ²Central Sericulture Research Institute, Berhampore, West Bengal,India. (Received May 27, 1980; )     

The nature of N-, P- and K-deficiency effects in rice

Effects of N-, P- and K-deficiencies on RNA synthesis in TN-1rice, Sonalika wheat and B-75 gram was examined at the molecularlevel. The melting temperatures of the chromatin of TN-1 rice,Sonalika wheat and B-75 gram was increased by deficiency conditions.In TN-1 rice the template activity of chromatin was reducedconsiderably, most remarkably in the case of the N-deficiency.The base composition of the newly synthesized RNA of the deficientroots also was altered. These changes were accompanied by anincrease in the histone-DNA ratio. There was, however, no qualitativechange in the histone patterns. The chromatin of deficient tissuesbound less actinomycin D than did that of the control, and thebinding of labelled cations and anions also decreased. In deficientplants endo- and exo-nuclease activities were enhanced, accompaniedby decreases in the intrinsic viscosity, sedimentation co-efficientand chain lengths of DNA. ¹This work was supported by a grant from the Department of AtmicEnergy, Government of India. ²Central Sericulture Research Institute, Berhampore, West Bengal,India. (Received May 27, 1980; )     

Quantitative analysis of HP1alpha binding to nucleosomal arrays

Elucidating how the metazoan genome is organised into distinct functional domains is fundamental to understanding all aspects of normal cellular growth and development. The "histone code" hypothesis predicts that post-translational modifications of specific histone residues regulate genomic function by selectively recruiting nuclear factors that modify chromatin structure. A paradigm supporting this hypothesis is the preferential binding of the silencing protein heterochromatin protein 1 (HP1) to histone H3 trimethylated at K9. However, a caveat to several in vitro studies is that they employed histone N-terminal tail peptides to determine dissociation constants, thus ignoring any potential role of DNA and/or the underlying chromatin structure in the recruitment of HP1. Using a well-defined in vitro chromatin assembly system (employing a 12-208 DNA template), we describe here, the use of a fluorescence spectroscopic method that enabled us to measure and quantify the relative binding affinities of HP1alpha to unmodified and variant nucleosomal arrays. Using this approach, we previously demonstrated that mouse HP1alpha (i) binds with high affinity to naked DNA, (ii) has an intrinsic affinity for highly folded chromatin, (iii) has a 2-fold higher affinity for nucleosomal arrays when H2A is replaced with H2A.Z, and (iv) binds to DNA or chromatin in a non-cooperative manner.     

Effect of salt on the binding of the linker histone H1 to DNA and nucleosomes

The linker histones are involved in the salt-dependent folding of the nucleosomes into higher-order chromatin structures. To better understand the mechanism of action of these histones in chromatin, we studied the interactions of the linker histone H1 with DNA at various histone/DNA ratios and at different ionic strengths. In direct competition experiments, we have confirmed the binding of H1 to superhelical DNA in preference to linear or nicked circular DNA forms. We show that the electrophoretic mobility of the H1/supercoiled DNA complex decreases with increasing H1 concentrations and increases with ionic strengths. These results indicate that the interaction of the linker histone H1 with supercoiled DNA results in a soluble binding of H1 with DNA at low H1 or salt concentrations and aggregation at higher H1 concentrations. Moreover, we show that H1 dissociates from the DNA or nucleosomes at high salt concentrations. By the immobilized template pull-down assay, we confirm these data using the physiologically relevant nucleosome array template.     

Studies on erythrocruorin. V. Nuclear magnetic resonance quadrupole relaxation study of sodium, calcium and chloride binding.

Metabolically labeled non-histone chromosomal proteins of high specific activity were fractionated on the basis of their sequential extractability from Krebs II chromatin with urea/salt solutions according to Bekhor et al. (1974a). The binding of each of these NHCP² classes to protein-free DNA and histone-DNA complexes (nucleohistone) was measured and compared to the binding to DNA substituted with 5-bromo-2′-deoxyuridine. After reconstitution of the interacting components, the binding of NHCP and histones was measured according to Scatchard formalism by titration of fixed amounts of DNA with increasing inputs of protein ligands under stringent conditions of 0.25 ionic strength, pH 8.0. Histone binding to either native DNA or BrUrd-substituted DNA was found to be essentially the same. In the presence of histones, the binding for all NHCP classes, except for medium 3 NHCP, was enhanced by an order of magnitude over the binding values for NHCP to DNA in the absence of histones. The binding of NHCP to DNA was thus strongly influenced by histones bound to DNA. A general and significant decrease in histone content in the complexes relative to increased NHCP binding was also apparent, with medium 3 NHCP having the greatest activity to weaken histone interaction with DNA and medium 0 the least. Enhancement in NHCP binding to BrUd-substituted DNA in the presence of histones was decreased to about 50% of the binding to control DNA. The distribution and quantity of DNA binding and non-DNA binding NHCP was also estimated by photochemical attachment to 33% BrUrd-substituted DNA in tryptophan-labeled chromatin and by direct binding assays. We have obtained 30% crosslinking for either histones or NHCP to DNA in stringently formed complexes. In histone-NHCP-DNA complexes, histone crosslinking remained unchanged, while that of NHCP increased to 70%. This is further evidence for a modification in the binding of NHCP to DNA in the presence of histones. The percentage of NHCP crosslinked to DNA in native chromatin ranged from 24% for medium 0 NHCP to 50% for medium 1 and 3 NHCP with an average of 35% for total NHCP. These results plus the direct binding assays indicate that NHCP, in addition to high affinity DNA binding, also interacts non-specifically to DNA and to proteins in chromatin. A mechanism is also being proposed to account for the observed BrUrd effects in chromatin.     

Binding of Epinephrine to Chromatin Components

To clarify the mechanism of the cellular DNA-breaking reaction of epinephrine (Ep), we examined the interaction between Ep and chromatin components. The Ep-binding activity of histone increased after the dissociation of histone subunits. The Ep bound to DNA increased with the increase of Ep concentration and pH. Solubilized chromatin, v bodies, showed Ep-oxidizing activity in the absence of Cu²⁺. The binding of Ep to v bodies occurred immediately after mixing and was highly specific. These data suggest the presence of some Ep-specific binding protein(s) in chromatin which oxidizes Ep and induces DNA breakage.     

Binding form of pollen mother cell protein in the nucleosomes of lily

We have previously reported the existence of pollen mother cell nuclear protein (PMCP) which appears during microsporogenesis in lily (Lilium spesiosum). It is very similar to mammalian testis specific H1 histone, H1t. In this paper, we describe the PMCP distribution in lily nucleosomes. Isolated nuclei were treated with micrococcal nuclease, and template active and inactive chromatin fractions were prepared. The nucleosome repeat length of pollen mother cells was determined to be 210 base pairs. The majority of the PMCP was found in the template inactive chromatin fraction, similar to other histones. PMCP was contained in the nucleosome monomer, but not in the core particle. However, PMCP was mainly found in the nucleosome dimer when slightly digested. Salt extraction from isolated nuclei indicated that PMCP and H1 histone share similar binding affinities to DNA. Judging from our results, it seems probable that PMCP links two core particles more strongly than H1 histone does. Since it is known that meiotic chromatin includes nick transferase and nuclease activity, one possible role of PMCP is the protection of its own chromatin. Other possible functions of PMCP are also discussed.     

Changes in chromatin of Daucus carota cells during embryogenesis

Cells of carrot (Daucus carota var. Rote Riesen) were cultured on media inductive and non-inductive for embryogenesis and analyzed for differences in their chromosomal proteins and chromatin template activity. Non-histone proteins were prepared from dehistonized chromatin and their properties were investigated. Non-histone proteins proved to be acidic and associated easily with calf thymus histone. Non-histone proteins were able to counteract the inhibitory effect of histone on DNA-directed RNA synthesis in vitro. Almost the same rate of restoration occurred regardless of the interaction between DNA and protein, when sufficient amounts of non-histone proteins were added. However, once the histone-DNA complex was established, the restoration by non-histone proteins at comparably lower concentration was poor. Another acidic protein, bovine serum albumin, had no effect on histone inhibited RNA synthesis. Also non-histone proteins enhanced the chromatin directed RNA synthesis more than 100%. The template activity of chromatin changed after the inductive treatment of embryo formation and induced cells showed higher template activity than non-indiiced controls after embryo cells were formed. Histone components were the same in inductive and non-inductive cells. On the other hand, there was a correlation between template activity and the stimulation by non-histone proteins of histone-inhibited RNA synthesis.     

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.     

CHANGES IN CHROMATIN TEMPLATE ACTIVITY AND THEIR RELATIONSHIP TO DNA SYNTHESIS IN MOUSE PAROTID GLANDS STIMULATED BY ISOPROTERENOL

Chromatin template activity of mouse parotid glands increases after a single injection of isoproterenol (IPR), a procedure that causes, after a lag period of 20 hr, a marked stimulation of DNA synthesis and cell division in salivary glands of rodents. The increase in chromatin template activity occurs as early as 1 hr and peaks between 6 and 10 hr after IPR, paralleling previously reported changes in the incorporation of uridine-³H into total cellular RNA of mouse parotids. Template activity was measured in vitro in a system in which parotid gland chromatin was incubated with an exogenous RNA polymerase isolated from Escherichia coli. Similar results were obtained when template activity of parotid gland chromatin was assayed using an homologous RNA polymerase from mouse liver. Chromatin template activity in mouse parotids was also studied after the administration of drugs capable of inducing in salivary glands both DNA synthesis and secretion or secretion alone. The results indicate that the increased chromatin template activity occurring 6 hr after IPR is related to the subsequent onset of DNA synthesis. Furthermore, the increased chromatin template activity caused by IPR is inhibited by the previous administration of puromycin, an inhibitor of IPR-stimulated DNA synthesis.     

In vitro interaction of 63-nickel(II) with chromatin and DNA from rat kidney and liver nuclei

The interaction of nickel(II) with chromatin was studied in vitro and in isolated nuclei from rat liver and kidney. Nickel(II) bound to chromatin, polynucleosomes (DNA + histone octamer protein complex), and to deproteinized DNA both in intact nuclei and in vitro. The amount of nickel(II) bound depended on the concentration of nickel(II), the presence of chromosomal proteins and the binding sites on DNA which provide a stable coordination environment for nickel(II). The binding of nickel(II) to chromatin and to DNA in whole nuclei was much slower than in vitro indicating that assessibility of the DNA binding sites was influenced by the presence of the nuclear membrane, nuclear matrix and nuclear proteins and/or by the condensed nuclear structure of chromatin. Since DNA containing bound nickel(II) was isolated from chromatin, nickel(II) directly interacted with stable binding sites on the DNA molecule in chromatin. Nickel(II) was associated with the histone and non-histone nuclear proteins as well as the DNA in rat liver and kidney chromatin. Nickel(II) was found to bind to calf thymus histones in vitro. Nickel(II)-nuclear protein and -DNA interactions were investigated by gel electrophoretic analysis of in vitro incubation products. Although nickel-histone and nickel-non-histone protein interactions were completely disrupted by the electrophoretic conditions, fluorography revealed the presence of inert nickel(II)-DNA and/or nickel(II)-DNA-protein complexes.     

Control of RNA synthesis by chromatin proteins.

The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA.     

Changes in enzymic activity during cultivation of human cells in vitro

The composition of chromatin, its template activity and the activity of certain chromatin-associated enzymes, including DNA polymerase (DP) and soluble RNase, DNase, DP and seryl tRNA synthetase, were examined in early and late passage of WI-38 cells and of WI-38VA13 cells.No significant changes in soluble RNase, DNase, seryl tRNA synthetase or soluble and chromatin-associated DP were found with increasing passage of WI-38 cells. The activity of seryl tRNA synthetase and DP in WI38VA13 cells was, however, significantly higher than WI-38 cells in all passages. A decline in RNA synthesizing activity of chromatin, an increase in the proportion of RNA and histone in chromatin, as well as an increase in the activities of ‘chromatin-associated enzymes’ (RNase, DNase, protease, nucleoside triphosphatase, DPN pyrophosphorylase) were noted in WI-38 cells with increasing passages. Although RNA synthesizing activity of chromatin from WI38VA13 cells was lower than that from WI-38 cells, the former also were much lower in ‘chromatin-associated enzymes’. An increase of chromatin-associated enzymes responsible for RNA, DNA and protein degradation in WI-38 cells in successive passages, and a much lower activity of these enzymes in WI-38VA13 cells (which have an indefinite doubling potential in vitro) suggests that an elevation in the activity of these enzymes, which would seriously interfere with the chromatin function, could result in ‘aging’ of WI-38 cells.