Evidence for the autophagy of microinjected proteins in HeLA cells.

Rhodamine-conjugated proteins were microinjected into living HeLa cells. Fluorescence microscopy was then employed to study their segregation from the cytoplasm into lysosomes. Results obtained in this way were verified when the corresponding unconjugated proteins were localized by autoradiographic, histological, and antibody-staining methods after their microinjection. Most injected proteins were segregated into cytoplasmic granular structures during their removal from cells. As evidence that these were autophagic vacuoles, they were found to contain no detectable acid phosphatase activity upon formation, after which they moved to the juxtanuclear position of lysosomes and appeared to fuse with them. The segregation of microinjected proteins exhibited a high degree of selectivity. The half-times of placement of individual exogenous proteins into cytoplasmic granules varied from 3 h to nearly 3 days, and one protein, hemoglobin, was never observed to enter them. Furthermore, endogenous HeLa proteins in a size fraction near 200,000 daltons were segregated much more rapidly than those in a fraction near 40,000 daltons. In these studies, rapid protein segregation appeared to take place by a mechanism of exclusion of the injected protein from numerous cytoplasmic domains.

Translational regulation of histone synthesis in the sea urchin strongylocentrotus purpuratus.

The pattern and schedule of histone synthesis in unfertilized eggs and early embryos of the sea urchin Strongylocentrotus purpuratus were studied using two-dimensional gel electrophoresis. After fertilization there is an abrupt change in the pattern of histone variant synthesis. Although both cleavage-stage (CS) variants. However, after fertilization, both CS and alpha messages are translated. Since alpha histone mRNA isolated from unfertilized eggs can be translated in vitro, the synthesis of alpha histone subtypes appears to be under translational control. Although the synthesis of alpha subtypes is shown here to occur before the second S phase after fertilization, little or no alpha histone is incorporated into chromatin at this time. Thus, early chromatin is composed predominantly of CS variants probably recruited for the most part from the large pool of CS histones stored in the unfertilized egg.

Turnover of basic chromosomal proteins in fertilized eggs: a cytoimmunochemical study of events in vivo.

The chromosomal complements of mouse oocytes, ova, and fertilizing sperm have been studied by immunofluorescence with specific antisera to the basic protein fraction of sperm nuclei and to histones H2b and H4, and by staining with ethidium bromide. These studies support the hypothesis, previously proposed (Rodman and Barth, 1979, Dev. Biol. 68:82-95), that the chromosomes of the oocyte in maturation incorporate unique basic protein(s) similar to those incorporated during spermiogenesis. That similarity is characterized, here, by immunologic cross-reactivity. The basic proteins of the fertilizing sperm nucleus and the cross-reactive moiety of the two haploid complements of the ovum are displaced simultaneously, shortly after sperm entry. However, because the unique basic proteins incorporated into the oocyte chromosomes do not, as in the spermatogenic sequence, entirely replace the histones, the maternal chromosomes display histones H2b and H4 at all postfertilization stages examined, whereas the decondensing paternal complement, for an interval before maturation of the pronuclei, contains neither sperm basic chromosomal proteins nor histones. Sequential staining of the same specimens with ethidium bromide revealed well-organized nuclear morphology of the residual DNA complex. Those observations suggest that, for an as yet undefined period in the transformation from spermatozoal to embryonic genome, the chromatin is devoid of a complement of basic proteins.

Different nucleosome structures on transcribing and nontranscribing ribosomal gene sequences.

Monomeric DNA lengths from Physarum nuclear chromatin occur in two subunit forms which differ from each other and from higher oligomers of nucleosomes in content of transcribed ribosomal DNA sequences. Labeled DNA restriction fragments from ribosomal RNA coding regions reanneal most rapidly with DNA from a monomeric subunit fraction. A particles, isolated from growing plasmodia and containing 144 base pairs of DNA in an extended conformation. Higher oligomers of nucleosomes are depleted in sequences from transcribing gene regions but are enriched in sequences from the nontranscribed central spacer of the ribosomal DNA palindrome. Nucleosome configuration on two 26S gene intervening sequences resembles that on adjacent coding regions.

Phosphorylation of nuclear protein early in the course of gene activation in lymphocytes.

Human lymphocytes treated with phytohemagglutinin undergo extensive gene activation, as evidenced by augmented synthesis of ribonucleic acids. This activation is preceded by an early stimulation in the rate of phosphorylation and dephosphorylation of nuclear proteins. This finding is consistent with a hypothesized role of phosphoproteins in the modification of chromatin structure and in modulation of the template activity of DNA in vivo.

Histone acetylation in insect chromosomes.

Acetylation of histones takes place along the salivary gland chromosomes of Chironomus thummi when RNA synthesis is active. It can be observed but not measured quantitatively by autoradiography of chromosome squashes. The "fixatives" commonly used in preparing squashes of insect chromosomes preferentially extract the highly acetylated "arginine-rich" histone fractions; the use of such fixatives may explain the reported absence of histone acetylation in Drosophila melanogaster.

Characteristic complements of nuclear nonhistone proteins in colonic epithelial tumors.

Nuclei were isolated from colonic epithelial tumors induced in rats by the administration of 1,2-dimethylhydrazine. The nuclei were fractionated according to buoyant density by centrifugation in discontinuous sucrose density gradients. Nuclei differing in density differ in size, nonhistone protein-to-DNA ratio, and DNA synthetic activity. Their distribution in a density gradient also reflects their histological localization in the layers of the intestinal mucosa, as judged by the nuclear capacity for [3H]thymidine incorporation into DNA in vivo. Different nuclear classes isolated from the tumors contain characteristic complements of nuclear nonhistone proteins. Particularly striking accumulations of two protein classes with molecular weights of ca. 44,000 and 62,000 occur during carcinogenesis. These proteins are not uniformly distributed throughout all nuclear classes derived from the tumors. They are not at all prominent in normal colonic epithelial nuclei or in epithelial cells surroundign the tumors, or in the liver nuclei of animals treated with 1,2-dimethylhydrazine. Procedures for the differential extraction of these protein classes are described. Similar nuclear proteins have been detected in human colonic tumors and in a human cell line (HT-29) derived from an adenocarcinoma of the colon. The selective accumulation of such proteins in colonic tumor nuclei may have diagnostic value.

Activation of sodium cyanate for selective inhibition of protein synthesis in cultured tumor cells.

Sodium cyanate, a selective inhibitor of protein synthesis in animal tumors in situ, has no comparable effect when added to tumor cells in culture. However, a rapid inhibition of protein synthesis in cultured tumor cells can be achieved by reaction of cyanate with the drug-metabolizing system of liver microsomes. Procedures are described for the induction, preparation, and testing of an active cytochrome P-450 fraction which converts cyanate to a short-lived dialyzable metabolite that selectively inhibits amino acid incorporation in tumor cells without a corresponding effect on protein synthesis in normal cells. The suppression of tumor protein synthesis is not due to a general toxicity reaction because thymidine incorporation into the DNA of tumor cells is not inhibited by the cyanate metabolite. When HeLa cells are exposed to sodium butyrate, a substance reported to suppress the malignant phenotype in several tumor cell lines, they lose their sensitivity to the cyanate metabolite. Chick fibroblasts which are normally insensitive to the cyanate metabolite become cyanate sensitive after transformation by the Schmidt-Ruppin strain of the Rous sarcoma virus.

Aberrant and nonrandom methylation of chromosomal DNA-binding proteins of colonic epithelial cells by 1,2-dimethylhydrazine.

The alkylating carcinogen 1,2-dimethylhydrazine (DMH) induces colonic tumors with high incidence. The sites of in vivo modification of target macromolecules were studied using [methyl-3H]DMH. Carcinogen binding to subcellular fractions of colonic epithelial cells was analyzed at time intervals ranging from 10 min to 36 hr, with particular emphasis on the alkylation of nuclear constituents. DMH modifies not only nucleic acids but also histones and other DNA-binding proteins in the target cells. Separation of the 3H-methylated amino acids showed aberrant methylation patterns after exposure to [3H]DMH, as compared with methylations observed with [methyl-3H]methionine as a natural methyl group donor. DMH-modified histone H1 contained methylated lysin, arginine, and histidine residues not normally found, and other histones had abnormal methylarginine contents. High-mobility-group proteins and other nuclear proteins contained methyllysine residues not normally detected. Proteins known to be associated with template-active and more accessible DNA sequences, such as the high-mobility group proteins and the multiacetylated forms of histones H3 and H4, were preferentially damaged after exposure to [3H]DmH. The result suggests that carcinogen-induced chromosomal damage is not random and may selectively affect proteins in the actively transcribing or replicating genes in the target cells. That damage affects the amino acids most likely to be involved in DNA binding.

Fractionation of nuclei and analysis of nuclear proteins of rat liver and Morris hepatoma 7777.

The contributions of nuclear populations to the total profile of nuclear proteins in a tissue were examined in normal rat liver and Morris hepatoma 7777. Comparison by sodium dodecyl sulfate polyacrylamide gel electrophoresis of phenol-soluble nuclear proteins from tumor and control liver revealed additional proteins of molecular weight 60,000, 100,00, and 135,000 and the loss of proteins of about 45,000 and 55,000 in the tumor. Subfractionation of liver nuclei on a 30 to 50% sucrose gradient yielded three nuclear classes with nearly identical complements of the phenol-soluble proteins. Similar fractionation performed on the hepatoma nuclei also produced three nuclear populations. In the hepatoma nuclei, several differences in the phenol-soluble proteins were found between the minor, slowly sedimenting nuclear fraction, and the two major fractions, while the two latter fractions were very similar in their protein composition. Histones derived from both tissues were also compared electrophoretically, indicating a decrease in the concentration of histone H1(0)in all nuclear classes derived from the tumor.

Dihydrotestosterone as a selective cellular/nuclear localization vector for anti-gene peptide nucleic acid in prostatic carcinoma cells.

Peptide nucleic acids (PNAs) are synthetic structural analogues of DNA and RNA that, if allowed to enter the cell, bind to the complementary polynucleotide sequence and inhibit DNA transcription and mRNA translation. Although PNAs have a very limited ability in penetrating nuclei of living cells, there are indications that covalent linkage of the PNA to appropriate vectors, e.g., a nuclear localization signal, permits access to the genome. Here we test the ability of dihydrotestosterone (T) covalently linked to PNA to act as a vector for targeting c-myc DNA to prostatic cancer cell nuclei. LNCaP cells, which express the androgen receptor gene, and DU145 cells, in which the androgen receptor gene is silent, offer a model to test this biologically active hormone as a cell-specific vector. T vector was covalently linked to the NH2-terminal position of a PNA complementary to a unique sequence of c-myc oncogene (PNAmyc-T). To localize PNAmyc-T and vector-free PNA within the cells, a rhodamine (R) group was attached at the COOH-terminal position (PNAmyc-R, PNAmyc-TR); cellular uptake was monitored by confocal fluorescence microscopy. PNAmyc-R was detected only in the cytoplasm of both prostatic cell lines, whereas PNAmyc-TR was localized in nuclei as well as in cytoplasm of LNCaP cells. In contrast, PNAmyc-TR uptake in DU145 cells was minimal and exclusively cytoplasmic. In LNCaP cells, MYC protein remained unchanged by exposure to vector-free PNAmyc, whereas a significant and persistent decrease was induced by PNAmyc-T. In DU145 cells, MYC expression was unaltered by PNAmyc with or without the T vector. Our data show that the T vector facilitates cell-selective nuclear localization of PNA and its consequent inhibition of c-myc expression. These findings suggest a strategy for targeting of cell-specific anti-gene therapy in prostatic carcinoma.

Phosphorlyation of H1 and H5 histones by cyclic AMP-dependent protein kinase reduces DNA binding.

Phosphorylation of H1 histones by cyclic AMP-dependent protein kinase may be an important transcriptional control mechanism. We have used affinity chromatography to examine the effect of phosphorylation by this enzyme on the DNA-binding properties of calf thymus H1 histones and two highly basic H1 homologues from condensed and transcriptionally silent nuclei: duck erythrocyte H5 and Strongylocentrotus purpuratus sperm H1. Without in vitro phosphorylation, all three histones were eluted from native DNA-Sephadex G-25 columns at salt concentrations which closely resembled those required to extract these histones from nuclei or chromatin. When a small portion of radioactively phosphorylated histone was chromatographed with untreated carrier histone, the phosphorylated species was consistently eluted from the DNA column at slightly lower salt concentrations than the main histone peak. Rechromatography experiments showed that in vitro phosphorylation of H1 can shift its elution position to lower salt concentrations.

Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences.

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.

Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription.

A new affinity chromatographic procedure for the separation of transcriptionally active nucleosomes has been used to study the changes that take place in chromatin structure along the c-fos and c-myc genes when RNA synthesis is inhibited. Mercury-affinity chromatography separates the sulfhydryl-reactive nucleosomes of transcriptionally active genes from the compactly beaded, non-reactive nucleosomes of transcriptionally inert DNA sequences. The new procedure also discriminates between nucleosomes that have "unfolded" to reveal the previously shielded SH groups of histone H3 and nucleosomes that bind to the mercury column because of their association with thiol-containing non-histone proteins located in the transcription unit. Both classes of Hg-bound nucleosomes contain the c-fos and c-myc sequences, but only when they are being transcribed. We compared the effects of alpha-amanitin and actinomycin D on the transcription of c-fos and c-myc with the effects of each inhibitor on the distribution of the corresponding oncogenic DNA sequences in the chromatographically separated nucleosome fractions. It was found that the inhibition of RNA polymerase II by alpha-amanitin (added at the peaks of c-fos or c-myc expression in serum-stimulated BALB/c 3T3 cells) resulted in a rapid loss of affinity of the oncogene-containing nucleosomes for the mercury column. There was no corresponding effect on the mercury-binding properties of nucleosomes containing 28 S ribosomal gene sequences, which continue to be transcribed by amanitin-resistant RNA polymerase I. Therefore, the binding of the c-fos and c-myc nucleosomes to the mercury column seems to depend upon reversible structural changes associated with their transcription. Surprisingly, there was no corresponding loss of affinity of the c-fos and c-myc nucleosomes for the mercury column when actinomycin D was employed to inhibit RNA synthesis, despite the fact that transcription of both genes had been arrested abruptly. Measurements of [3H]actinomycin D binding show its preferential intercalation into the transcriptionally active nucleosomes. We suggest that the intercalation of actinomycin D into the DNA of active nucleosomes can lock the transcription complex into an "unfolded" but potentially active configuration. This was confirmed by run-off transcription assays showing a restoration of c-fos and c-myc RNA synthesis when actinomycin D was displaced by proflavine.

Contrasting effects of PNA invasion of the chimeric DMMYC gene on transcription of its myc and PVT domains.

A peptide nucleic acid (PNA) complementary to a unique DNA sequence in the second exon of the human myc proto-oncogene was tested for its effects on transcription in colonic adenocarcinoma cells in which myc had been amplified and rearranged. A prominent rearrangement in this human cell line (COLO320-DM) involves the insertion of exon 1 of the PVT gene, which is normally located 57 kb downstream, into the first myc intron. We compared the effects of PNA invasion of the resulting chimeric gene (DMMYC) on sense and antisense transcription of its myc and PVT domains. Run-on transcription experiments showed that PNA binding to the unique myc sequence was highly specific and strongly inhibited sense transcription of four unique myc sequences downstream of the PNA.DNA hybridization site, the extent of inhibition at each sequence depending on the duration of exposure to PNA, and the distance between the downstream myc sequence and the PNA block. The same PNA also inhibited antisense transcription of unique myc sequences upstream of the binding site, confirming that transit of the RNA polymerase II complexes was impaired in both directions. The inhibitory effect of PNA on upstream antisense transcription extended beyond the recombination site into the contiguous PVT domain of the chimeric DMMYC gene. In contrast, the same PNA did not inhibit PVT transcription in a cell line (Raji lymphoma) in which PVT rearrangement did not involve the myc locus.

High resolution microanalysis and three-dimensional nucleosome structure associated with transcribing chromatin.

The nucleosome is the ubiquitous and fundamental DNA-protein complex of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Biophysical studies have implicated changes in nucleosome structure from chromatin that is quiescent to active in transcription. Since DNA within the nucleosome contains a high concentration of phosphorus whereas histone proteins do not, the nucleosome structure is amenable to microanalytical electron energy loss mapping of phosphorus to delineate the DNA within the protein-nucleic acid particle. Nucleosomes associated with transcriptionally active genes were separated from nucleosomes associated with quiescent genes using mercury-affinity chromatography. The three-dimensional image reconstruction methods for the total nucleosome structure and for the 3D DNA-phosphorus distribution combined quaternion-assisted angular reconstitution of sets of single particles at random orientations and electron spectroscopic imaging. The structure of the active nucleosome has the conformation of an open clam-shell, C- or U-shaped in one view, elongated in another, and exhibits a protein asymmetry. A three-dimensional phosphorus map reveals a conformational change in nucleosomal DNA compared to DNA in the canonical nucleosome structure. It indicates an altered superhelicity and is consistent with unfolding of the particle. The results address conformational changes of the nucleosome and provide a direct structural linkage to biochemical and physiological changes which parallel gene expression.