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T Boulikas

Publications and source records attributed to T Boulikas.

At least 37 records · Page 2Linked to original sources
PubMed1990

Studies on protein poly(ADP-ribosylation) using high resolution gel electrophoresis.

Analysis of poly(ADP-ribose) synthesized in cellular lysates or in isolated nuclei on 100-cm-long thin gels of 20% polyacrylamide, 2.5 M urea permits determination of the exact size of poly(ADP-ribose) molecules using labeled oligonucleotides as molecular weight markers. The size and concentration of poly(ADP-ribose) molecules increase at time intervals during its synthesis. Differences in the concentration of poly(ADP-ribose) size classes among cell lines are also shown. Inhibition of poly(ADP-ribose) degradation by ethacridine that directly interacts with the polymer and inhibits its hydrolysis by poly(ADP-ribose) glycohydrolase shows a dramatic increase in both polymer size and concentration. Use of alkaline conditions for the hydrolysis of poly(ADP-ribose)-protein linkages reveals a specific shortening of all size classes of poly(ADP-ribose) compared with its size in preparations obtained by extensive digestion of nuclei with nucleases, RNases, and proteases.

Animals↗
PubMed1990

Poly(ADP-ribosylated) histones in chromatin replication.

Poly(ADP-ribosylation) of histones and several other nuclear proteins seem to participate in nuclear processes involving DNA strand breaks like repair, replication, or recombination. This is suggested from the fact that the enzyme poly(ADP-ribose) polymerase responsible for this modification is activated by DNA strand breaks produced in these nuclear processes. In this article I provide three lines of evidence supporting the idea that histone poly(ADP-ribosylation) is involved in chromatin replication. First, cellular lysates from rapidly dividing mouse or human cells in culture synthesize a significant number of oligo- in addition to mono(ADP-ribosylated) histones. Blocking the cells by treatment of cultures with 5 mM butyrate for 24 h or by serum or nutrient depletion results in the synthesis of only mono- but not of oligo(ADP-ribosylated) histones under the same conditions. Thus, the presence of oligo(ADP-ribosylated) histones is related to cell proliferation. Second, cellular lysates or nuclei isolated under mild conditions in the presence of spermine and spermidine and devoid of DNA strand breaks mainly synthesize mono(ADP-ribosylated) histones; introduction of a small number of cuts by DNase I or micrococcal nuclease results in a dramatic increase in the length of poly(ADP-ribose) attached to histones presumably by activation of poly(ADP-ribose) polymerase. Free ends of DNA that could stimulate poly(ADP-ribosylation) of histones are present at the replication fork. Third, putatively acetylated species of histone H4 are more frequently ADP-ribosylated than nonacetylated H4; the number of ADP-ribose groups on histone H4 was found to be equal or exceed by one the number of acetyl groups on this molecule. Since one recognized role of tetraacetylated H4 is its participation in the assembly of new nucleosomes, oligo(ADP-ribosylation) of H4 (and by extension of other histones) may function in new nucleosome formation. Based on these results I propose that poly(ADP-ribosylated) histones are employed for the assembly of histone complexes and their deposition on DNA during replication. Modified histones arise at the replication fork by activation of poly(ADP-ribose) polymerase by unligated Okazaki fragments.

Animals↗
PubMed1990

Increase in histone poly (ADP-ribosylation) in mitogen-activated lymphoid cells.

Poly (ADP-ribosylated) histones appear to be intermediates in nuclear processes that involve DNA strand breaks. We have studied histone ADP-ribosylation in cellular lysates from activated human lymphoid cells in culture. Modified histones differing in the number of ADP-ribose groups gave separate bands upon two-dimensional gel electrophoresis. Cellular lysates from control cells contained histones modified with 1 to 15 ADP-ribose groups. Stimulation of the cells during culture with phytohemagglutinin (PHA) or a phorbol ester (TPA) as well as combinations of these two reagents led to a significant increase in the upper limit number of ADP-ribose groups attached to histones in the presence of divalent metal ions. Hyper (ADP-ribosylated) H2B carrying at least 32 ADP-ribose groups gave a distinctly characteristic pattern on two-dimensional gels showing that highly ordered enzymatic steps are followed for its synthesis. Moreover, it was found that PHA and/or TPA induces branching of the poly (ADP-ribose) on H2B. The increase in histone poly (ADP-ribosylation) following lymphocyte activation was less dramatic during incubation of cellular lysates in the absence of divalent metal ions. The increased histone modification observed in this study may result from an increase in cell proliferation during activation of lymphoid cells. The finding that the number of ADP-ribose groups on H4 equals or exceeds by one the number of acetyl groups suggests that the two modifications may share common functions.

Calcimycin↗
PubMed1989

DNA strand breaks alter histone ADP-ribosylation.

Histone ADP-ribosylation was studied using two-dimensional gel electrophoresis after cleavage of the nuclear DNA with nucleases. Modified histones carrying different numbers of ADP-ribose groups form a ladder of bands above each variant histone. Cellular lysates containing unfragmented DNA mainly synthesize mono(ADP-ribosylated) histones. Cleavage of the DNA with either DNase I or micrococcal nuclease to fragments of an average size of 10-20 kilobases (kb) dramatically induces the formation of poly(ADP-ribosylated) species of histones in nuclei. As the number of DNA strand breaks produced by either DNase I or micrococcal nuclease increases and a great number of DNA cuts is introduced (fragments of 0.4-0.2 kb), the size of the poly(ADP-ribose) chains on the histones decreases. Finally, in the presence of 10 mM cAMP as an inhibitor of poly(ADP-ribose) glycohydrolase, human lymphoid nuclei synthesize hyper(ADP-ribosylated) histone H2B with at least 40 ADP-ribose groups attached to it. Lateral ladders emanating at precise points of the linear ladder on hypermodified H2B can arise from branching of poly(ADP-ribose) or from multiple monomodifications of glutamic (or aspartic) acid residues. Branching or de novo monomodifications occur after a precise number of ADP-ribose groups have been added to a histone molecule. Poly(ADP-ribosylated) histones thus appear to be intermediates in nuclear processes involving DNA strand breaks.

Adenosine Diphosphate Ribose↗
PubMed1988

At least 60 ADP-ribosylated variant histones are present in nuclei from dimethylsulfate-treated and untreated cells.

The level of histone adenosine diphospho (ADP) ribosylation was studied in isolated nuclei from mouse myeloma cells in culture. The cells were treated with dimethylsulfate (DMS), a DNA-methylating agent, and histones were analyzed using two-dimensional gel electrophoresis. Seventeen or more bands probably representing mono-to heptadeca (ADP-ribosylated) histones could be visualized for each major variant histone. DMS treatment, by increasing the number of chromatin sites undergoing repair, greatly enhanced histone ADP-ribosylation. When histones were labeled in a cell lysate rather than in isolated nuclei, mono- and oligo(ADP-ribosylated) histone forms prevailed. The presence of approximately 87 ADP-ribosylated variant histone forms in cell lysates and of approximately 170 in isolated nuclei is shown for the first time in this work. Previous studies show multiple ADP-ribosylated forms for only histone H1. The theoretical number of variegated nucleosomes is thus much higher than previously thought, provided that histone-histone contacts are not disrupted at up to a certain level of histone ADP-ribosylation.

Adenosine Diphosphate Ribose↗
PubMed1986

Nucleosomes are assembled into discrete size structures by histone H1 in vitro.

The involvement of histone H1 in the formation and maintenance of higher order chromatin structures in vitro was investigated biochemically. Addition of exogenous histone H1 to isolated calf thymus mononucleosomes in low ionic strength buffer resulted in the formation of electrophoretically distinct mononucleosome assemblies (supernucleosomes). The smaller supernucleosomes were composed of about 12, 18, 24, or 30 nucleosomes and one to two molecules of histone H1 per nucleosome. It was difficult to determine accurately the size of the larger supernucleosomes, but their bands from native gels contained probably between 60 and 300 nucleosomes or more. Similar supernucleosome size classes were also obtained when oligonucleosomes instead of mononucleosomes were employed. When the assembly of mono- and oligo-nucleosomes with histone H1 took place in 0.15 M NaCl, discrete supernucleosomes containing only mono- or di-nucleosomes, but not a mixture of both, were formed. It is proposed that the small supernucleosomes containing oligomers of 6 nucleosomes may represent integral multiples of the second-order chromatin structural subunit, whereas the larger supernucleosomes containing about 60 to 300 or more nucleosomes may correspond to chromatin domains or third-order chromatin structures observed by other techniques.

Animals↗
PubMed1986

Protein-protein and protein-DNA interactions in calf thymus nuclear matrix using cross-linking by ultraviolet irradiation.

Nuclear matrices from calf thymus contained 30-50 protein species with one prominent band at 70 kilodaltons tentatively identified by its isoelectric point, apparent molecular weight, charge modification, and abundance as bovine lamin. The amount of DNA present in the matrix fraction was strongly dependent on the extent of digestion of the nuclei by micrococcal nuclease. The size of the DNA was higher than two kilobase pairs, although the chromatin DNA had been digested down to short oligonucleosomes. The lamin band was preferentially dissociated from isolated matrices during repeated treatment by 2 M NaCl or 5 M urea. Irradiation of calf thymus nuclear matrices at 313 nm induced protein-protein and protein-DNA cross-linking, as well as double-strand breaking of DNA, presumably at unprotected, protein-free regions. Lamin protein was more dramatically affected than other protein species by ultraviolet (UV) irradiation. In situ DNA hydrolysis, after the separation of the cross-linked matrix components on polyacrylamide-sodium dodecyl sulfate gels, followed by two-dimensional electrophoresis, showed lamin to be the major protein that was cross-linked to the DNA. Lamin molecules were also cross-linked by UV light to each other to form lamin homo-oligomers. A discrete size DNA fragment of approximately 450 base pairs is protected by lamin homo-oligomers from breakdown during UV irradiation. It is proposed that the direct contact between lamin and DNA found in this study is responsible for anchoring chromatin loops (domains) to a stable, immobile matrix structure.

Animals↗
PubMed1985

Electrophoretic separation of histones and high-mobility-group proteins on acid-urea-Triton gels.

The electrophoretic mobilities of calf thymus histones and high-mobility-group (HMG) nonhistone proteins were studied on a newly modified polyacrylamide gel containing acetic acid, urea, and the nonionic detergent Triton X-100 in combination with glycine in the electrode buffer. This gel system avoids stacking gel, photopolymerization of acrylamide, and preelectrophoresis. Under extremely low Triton concentrations some H3 variant forms (H3.1) were preferentially separated by their slower migration from bulk H3. Under increasing concentrations of Triton in the gel in the presence of 3 or 6 M urea, the mobilities of H2A.1, H3.2, H2A.2, H4, and H2B were sequentially retarded. The mobilities of H1 and HMGs remained virtually unchanged under all conditions. This gel system is able to resolve charge-modified histones.

Acetates↗
PubMed1985

Interaction of histone H1 with oligonucleosomes in vitro provides a convenient method for isolating mononucleosomes.

The interaction of histone H1 with oligonucleosomes was studied in 0.15 M NaCl. Exogenous calf thymus H1 was added to a mixture of oligonucleosomes, soluble in 0.15 M NaCl, and the partially precipitated chromatin was removed by centrifugation. A strong preference of H1 for the longer nucleosomes in the mixture was observed causing their precipitation and leaving the shorter oligonucleosomes preferentially soluble. Histone H1 could even discriminate in its binding between mono- and di-nucleosomes, binding to dinucleosomes and leaving the mononucleosomes preferentially soluble. On this basis a convenient method was developed for the rapid isolation of mononucleosomes. The fidelity of H1 reconstitution to the oligonucleosomes under these conditions was suggested employing zero-length carbodiimide cross-linking and radioiodinated H1. This fraction of mononucleosomes displays significantly higher levels in the more hydrophilic H3.2 and H3.3, as well as H2A.2 and H2A.3 variant histone forms, compared with bulk chromatin. The, presumably, lower affinity of histone H1 for this subfraction of mononucleosomes is discussed.

Animals↗
PubMed1981

A highly sensitive technique for staining DNA and RNA in polyacrylamide gels using silver.

A technique is described for staining DNA in polyacrylamide gels with silver. It is rapid, requiring about 30 min for whole staining and development procedure, very simple and at least 20 times more sensitive than ethidium bromide for the staining of double-stranded DNA in polyacrylamide gels. This technique can also be applied for the staining of denatured, single-stranded DNA as well as RNA after their electrophoretic separation on polyacrylamide gels, having the same sensitivity as for double-stranded DNA fragments.

Bacteriophage lambda↗
PubMed1980

A nonamer of histones in chromatin.

The results of dimethyl suberimidate cross-linking experiments demonstrate that histone H1 can be cross-linked quantitatively to the histone octamer of mononucleosomes to yield a histone nonamer. By combining our cross-linking procedure with two-dimensional electrophoretic techniques, we show further that it is possible to trace the nucleosomal origins of a spectrum of cross-linked chromatin products.

Animals↗
PubMed1980

Points of contact between histone H1 and the histone octamer.

The topography of the interaction between histone H1 and the histone octamer has been investigated. Bovine thymus nuclei or enzymatically fragmented chromatin were treated 1-ethyl-3(3-dimethylaminopropyl)carbodiimide, which catalyzes the formation of covalent bonds between residues of proteins in electrostatic contact. Histone H1-core histone dimers were identified and the segments of molecules participating in crosslinking were elucidated. The results demonstrate that the major histone H1-core histone dimer generated upon carbodiimide crosslinking of intact nuclei, chromatin, or mononucleosomes consists of the segment of histone H1 containing amino acids 74-106 crosslinked to the segment of histone H2A containing amino acids 58-129. Thus, the central globular region of histone H1 intimately contacts the histone octamer. Besides histone H1-H2 dimers, two other histone H1-containing crosslinked products were detected. In these instances, the segments of histone H1 molecules containing amino acids 1-72 were shown to participate in crosslinking. The histone H1 contact points defined here all occur within mononucleosomes and not between nucleosomes. These results permit the formulation of a testable model for the arrangement of histone H1 along polynucleosome chains.

Amino Acid Sequence↗
PubMedDate not supplied

Immunogene therapy of recurrent glioblastoma multiforme with a liposomally encapsulated replication-incompetent Semliki forest virus vector carrying the human interleukin-12 gene--a phase I/II clinical protocol.

Glioblastoma multiforme (GBM) is an incurable brain tumor resistant to standard treatment modalities such as surgery, radiation, and chemotherapy. Since recurrent GBM tends to develop predominantly within the infiltrative rim surrounding the primary tumor focus, novel therapy strategies need in addition to focal tumor destruction to target this somewhat diffuse area. This is a phase I/II clinical study in adult patients with recurrent GBM which is aimed at evaluating biological safety, maximum tolerated dose, and antitumor efficacy of a genetically modified replication-disabled Semliki forest virus vector (SFV) carrying the human interleukin 12 (IL-12) gene and encapsulated in cationic liposomes (LSFV-IL12). The vector will be administered in doses of 1 x 10(7)-1 x 10(9) infectious particles by continuous intratumoral infusion, thus exploiting the advantages of convection-enhanced drug delivery in the brain. The present protocol is also designed to investigate systemic and local immune response and to identify factors predicting tumor response to LSFV-IL12 therapy, such as volume of extracellular space of the tumor, volume of contrast enhancing lesion, and immune status of the patients. SFV, an insect alphavirus, infects mitotic and non-mitotic cells and triggers apoptosis in tumor cells within 48-72 h. Preclinical work with the LSFV-IL12 vector in breast and prostate cancer animal models demonstrated its biosafety and some antitumor efficacy. An ongoing phase I clinical study in patients with melanoma and renal cell carcinoma seems also to confirm the biosafety of intravenously administered vectors. This protocol will be the first study of SFV-IL12 therapy of human recurrent GBM.

Adult↗
PubMedDate not supplied

Resistance of ADP-ribosylated histones and HMG proteins to proteases.

Calf thymus histones (individually isolated or mixtures) and high mobility group proteins were ADP-ribosylated in vitro using [32P]NAD+ and immobilized purified poly(ADP-ribose) polymerase. The modified histones were then subjected to V8 protease or alpha-chymotrypsin digestion and the resulting peptides were separated by electrophoresis on acetic acid-urea-Triton gels. It was found that in vitro ADP-ribosylated histones were much more resistant to proteases than unmodified histones. A similar approach was applied to histones modified by the endogenous poly(ADP-ribose) polymerase in permeabilized NS-1 mouse myeloma cells in culture. In this case, the proteases could not discriminate between modified and unmodified histones and putative mono(ADP-ribosyl)ated peptides appeared in a digestion frame corresponding to that of bulk peptides. These differences are most probably due to the specificity or number of ADP-ribose groups added to the histones by the endogenous or exogenous poly(ADP-ribose) polymerase. Thus, depending on the size of poly(ADP-ribose) attached to nuclear proteins, these modified proteins might display different degrees of resistance to proteolysis.

ADP Ribose Transferases↗
PubMedDate not supplied

Poly(ADP-ribose) synthesis in blocked and damaged cells and its relation to carcinogenesis.

There is compelling evidence showing that repair of DNA damage depends on the synthesis of poly(ADP-ribose) molecules at specific sites on histones and other proteins in nuclei of injured cells. In the present study, we have studied the effect of long-term exposure of mouse cells to nicotinamide and various cell cycle blockers on the ability of the cells to increase their levels of poly(ADP-ribose) in response to DNA methylation damage with dimethylsulfate (DMS). Of the cell cycle blockers used, hydroxyurea (HU) and cytosine arabinofuranoside (ara-C) inhibit DNA elongation at the replication fork and cause the appearance of small DNA molecules, whereas butyrate and colcemid block cells without interfering with DNA synthesis. In addition, cells were treated with nicotinamide, an inhibitor of poly(ADP-ribose) polymerase but also a precursor in NAD+ biosynthesis. Long-term exposure of cultured cells to these agents was followed with a short-term damage with DMS. The size-class distribution and concentration of poly(ADP-ribose) molecules were determined using high resolution polyacrylamide gel electrophoresis and were found to contain 1 to more than 30 ADP-ribosyl groups. On the contrary, histones from blocked cell nuclei were found to be mono- and oligo(ADP-ribosyl)ated. Thus, the large molecules of poly(ADP-ribose) were associated with nonhistone proteins and most likely with the enzyme pADP-R polymerase. DMS damage caused an increase in the levels of poly(ADP-ribose) that was synthesized in lysates from cells treated with any one drug alone. On the other hand, a dramatic decrease in total protein poly(ADP-ribosyl)ation resulted from DMS damage of cells treated with nicotinamide + HU or nicotinamide + ara-C. This decrease was not observed in combinations of nicotinamide with cell-cycle blockers that do not directly interfere with DNA synthesis (butyrate and colcemid). We suggest that nicotinamide + ara-C or nicotinamide + HU might be used as effective antineoplastic treatments by virtue of their ability simultaneously to damage DNA and reduce poly(ADP-ribosyl)ation and presumably DNA repair. A model for the facilitation of DNA repair by poly(ADP-ribosyl)ation of histones and of poly(ADP-ribose) polymerase is presented.

Animals↗
PubMedDate not supplied

Relation between carcinogenesis, chromatin structure and poly(ADP-ribosylation) (review).

Poly(ADP-ribose) is a naturally occurring nuclear macromolecule resembling nucleic acids. It is synthesized from NAD+ on histones and a few other nuclear proteins. Its function, although not completely understood, might be to alter chromatin structure and to regulate the activity of proteins involved in the metabolism of DNA strand breaks such as ligase II, and topoisomerase I. In addition, poly(ADP-ribose) modifies proteins involved in gene expression such as acetylated histones. HMG proteins, and T antigen. The enzyme poly(ADP-ribose) polymerase responsible for this modification has the unique property of requiring nicks or free ends on the DNA for its activity and of being automodified. The automodified enzyme, presumably found at the vicinity of DNA strand breaks at damaged chromatin sites, could remove histones from DNA and attract enzymes that have an affinity for poly(ADP-ribose) such as ligase II or poly(ADP-ribose) glycohydrolase, the polymer-degrading enzyme. Alterations in chromatin structure alter gene expression and seem to be involved in repair, replication, and recombination and in changing DNA superhelical density, intermediate steps in molecular carcinogenesis. Experiments with cells in culture and laboratory animals show that inhibition of poly(ADP-ribosylation) alters transformation and tumorigenicity brought about by a great number of carcinogenic agents. Cancer can be caused by the accumulation of unrepaired DNA strand breaks in the cell accelerating gene rearrangements, deletions, insertions and amplifications. Repair of DNA strand breaks shows an absolute dependence upon the rapid synthesis and degradation of poly(ADP-ribose). The polymer has a very short half life indeed. Data are reviewed on changes in chromatin structure and function caused by histone and nonhistone poly(ADP-ribosylation). The link of this modification to transformation, tumorigenesis, development, replication and gene expression is examined. A model is proposed to explain the effect of poly(ADP-ribosylation) on chromatin structure at the molecular level. Mono- and oligo(ADP-ribosylated) histones present in nuclei under physiological conditions are proposed to functions, like acetylated histones, in maintaining chromatin loops into transcriptionally active structures. On the other hand, poly(ADP-ribosylated) histones and poly(ADP-ribosylated) enzymes such as DNA and RNA polymerases, suggested to be modified from in vitro studies, might only appear in cells that have been heavily damaged by carcinogen. Their function might be to remove histones from DNA in order to facilitate repair and to shut down transcription and replication.

Animals↗