Fractionation and characterization of chromosomal proteins by the hydroxyapatite dissociation method

Extracting histones for the specific purpose of label-free MS

Extracting histones from cells is the first step in studies that aim to characterize histones and their post‐translational modifications (hPTMs) with MS. In the last decade, label‐free quantification is more frequently being used for MS‐based histone characterization. However, many histone extraction protocols were not specifically designed for label‐free MS. While label‐free quantification has its advantages, it is also very susceptible to technical variation. Here, we adjust an established histone extraction protocol according to general label‐free MS guidelines with a specific focus on minimizing sample handling. These protocols are first evaluated using SDS‐PAGE. Hereafter, a selection of extraction protocols was used in a complete histone workflow for label‐free MS. All protocols display nearly identical relative quantification of hPTMs. We thus show that, depending on the cell type under investigation and at the cost of some additional contaminating proteins, minimizing sample handling can be done during histone isolation. This allows analyzing bigger sample batches, leads to reduced technical variation and minimizes the chance of in vitro alterations to the hPTM snapshot. Overall, these results allow researchers to determine the best protocol depending on the resources and goal of their specific study. Data are available via ProteomeXchange with identifier PXD002885.

Hitchhiker antigens: Inconsistent ChIP results, questionable immunohistology data, and poor antibody performance may have a common factor

Questionable data and poor antibody performance may have a common factor: antigens “hitchhiking” on the very antibodies designed to target them. Here I focus on histone hitchhikers and their antibodies, given the impact of chromatin immunoprecipitation on our understanding of DNA regulation. Caused by a lack of stringency during antibody purification, hitchhikers will impede important advances in chromatin research and therapeutics derived from that research, if similar circumstances in the study of lupus decades ago are any guide. Evidence of this phenomenon is reviewed, purification modifications for antibody manufacturing are suggested, and a histone hitchhiker detection procedure is provided.

Effects of DNA methylation on nucleosome stability

Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted nucleosome reconstitution experiments in conjunction with high-throughput sequencing on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin.

NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein

The post-translational methylation of α-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L331–2, but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be α-N-methylated3–10. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of α-N-methylation has been identified3, 11. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects3, 11, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating they may be targets of the same, unknown enzyme3,12. The initiating Met is cleaved, and the exposed α-amino group is mono-, di-, or trimethylated. Here we report the discovery of the first α-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET/TAF-I/PHAPII and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants3, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.

Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications

Post-translational modifications (PTMs) of histones play a role in modifying chromatin structure for DNA-templated processes in the eukaryotic nucleus, such as transcription, replication, recombination and repair; thus, histone PTMs are considered major players in the epigenetic control of these processes. Linking specific histone PTMs to gene expression is an arduous task requiring large amounts of highly purified and natively modified histones to be analyzed by various techniques. We have developed robust and complementary procedures, which use strong protein denaturing conditions and yield highly purified core and linker histones from unsynchronized proliferating, M-phase arrested and butyrate-treated cells, fully preserving their native PTMs without using enzyme inhibitors. Cell hypotonic swelling and lysis, nuclei isolation/washing and chromatin solubilization under mild conditions are bypassed to avoid compromising the integrity of histone native PTMs. As controls for our procedures, we tested the most widely used conventional methodologies and demonstrated that they indeed lead to drastic histone dephosphorylation. Additionally, we have developed methods for preserving acid-labile histone modifications by performing non-acid extractions to obtain highly purified H3 and H4. Importantly, isolation of histones H3, H4 and H2A/H2B is achieved without the use of HPLC. Functional supercoiling assays reveal that both hyper- and hypo-phosphorylated histones can be efficiently assembled into polynucleosomes. Notably, the preservation of fully phosphorylated mitotic histones and their assembly into polynucleosomes should open new avenues to investigate an important but overlooked question: the impact of mitotic phosphorylation in chromatin structure and function.

Enrichment and characterization of histones by two-dimensional hydroxyapatite/reversed-phase liquid chromatography-mass spectrometry

Here we report a novel two-dimensional liquid chromatography-mass spectrometry (2D LC-MS) method that combines offline hydroxyapatite (HA) chromatography with online reversed-phase liquid chromatography-mass spectrometry (HA/RP LC-MS). The 2D LC-MS method was used to enrich and characterize histones and their posttranslational modifications. The 2D HA/RP LC-MS approach separates histones based on their relative binding affinity to DNA and relative hydrophobicity. HA/RP separations showed improvement in the number of histone isoforms detected as compared with one-dimensional RP LC-MS of acid-extracted histones. The improved histone fractionation resulted in better detection of lower abundant histone variants as well as their posttranslationally modified isoforms. Histones eluted from the HA/RP in the following order: H1, H2A/H2B heterodimers followed by H3/H4 heterotetramers, as predicted from their spatial organization in nucleosomes for binding affinity to DNA. Comparison between HA-purified and acid-extracted histones revealed similar histone profiles with the exception that the HA fractions showed a greater number of H1 isoforms. Two elution conditions were also examined: batch elution and salt gradient elution. Although both elution techniques were able to fractionate the histones sufficiently, the salt gradient approach has the most potential for purification of selected histone isoforms.

Mass spectrometry-based strategies for characterization of histones and their post-translational modifications

Due to the intimate interactions between histones and DNA, the characterization of histones has become the focus of great attention. A series of mass spectrometry-based technologies have been dedicated to the characterization and quantitation of different histone forms. This review focuses on the discussion of mass spectrometry-based strategies used for the characterization of histones and their post-translational modifications.

The dual activity of pyruvate kinase type M2 from chromatin extracts of neoplastic cells

Pyruvate kinase type M(2) from Morris hepatoma 7777 tumour cell nuclei and cytosol, in contrast to types L and M(2) from nuclei and cytosol of normal rat liver, shows the histone H(1) kinase activity. Moreover, in the presence of L-cysteine and without ADP it converts 2-phosphoenolpyruvate (PEP) to pyruvate while in the presence of L-arginine or L-histidine does not. L-Cysteine markedly stimulates the activity of histone H(1) kinase transferring a phosphate group from PEP to, as results suggested, the epsilon -amino group of L-lysine of histone H(1). This, L-cysteine which is known to inhibit the activity of pyruvate kinase type M(2) from neoplastic cells transfering a phosphate from PEP to ADP, can act as a control factor champing the direction of enzymatic reaction in cancer cells.

A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis

The centromere, a differentiated region of the eukaryotic chromosome, mediates the segregation of sister chromatids at mitosis. In this study, a Saccharomyces cerevisiae chromosome mis-segregation mutant, cse4-1, has been isolated and shown to increase the nondisjunction frequency of a chromosome bearing a mutant centromere DNA sequence. In addition, at elevated temperatures the cse4-1 allele causes a mitosis-specific arrest with a predominance of large budded cells containing single G2 nuclei and short bipolar mitotic spindles. The wild-type gene, CSE4, is essential for cell division and encodes a protein containing a domain that is 64% identical to the highly conserved chromatin protein, histone H3. Biochemical experiments demonstrate that CSE4p has similar DNA-binding characteristics as those of histone H3 and might form a specialized nucleosome structure in vivo. Interestingly, the human centromere protein, CENP-A, also contains this H3-like domain. Data presented here indicate that CSE4p is required for proper kinetochore function in yeast and may represent an evolutionarily conserved protein necessary for assembly of the unique chromatin structure associated with the eukaryotic centromere.

Extraction and partial characterization of non-histone nuclear proteins of Schistosoma mansoni

A pool of nuclear proteins from adult worms of Schistosoma mansoni was analyzed for amino acid composition and found to be compatible with high mobility group (HMG) proteins. One of the schistosome HMG proteins was identified as HMG 2 by one-dimensional and two-dimensional PAGE. Stage-specific differences in the HMG-like protein composition were encountered when adult worms were compared to schistosomula, the larval form. Immobilization of the adult male and female nuclear proteins onto nitrocellulose, followed by hybridization against 32P-F-10, a schistosome sex specific gene encoding a major egg shell protein, revealed distinct banding patterns. On the other hand, a synthetic oligonucleotide, derived from the 3' untranslated end of the F-10 gene and possibly containing one regulatory element of the gene, bound mainly to male low MW proteins.

The presence of N-glycosylated proteins in cell nuclei

The protein-DNA crosslinking capability of cis-dichloro diammineplatinum has been exploited to check the intranuclear location of N-glycosylated proteins. When intact liver cells were treated with this reagent, a number of glycoproteins, recognized by Concanavalin A, have been shown to become crosslinked to DNA; many of them have been recognized as nuclear matrix components. The recognition by this lectin was abolished by treatment with N-glycosidase F, showing the presence of N-glycosidic bonds between the sugar moiety and the protein. Most of the glycoproteins appeared to have high mannose oligosaccharide chains, but sialic acid containing oligosaccharides were also identified.

Formation of DNA adducts in F-344 rats after oral administration or inhalation of [14C]methyl bromide

The genotoxic effects of methyl bromide were investigated in a DNA-binding study. [14C]Methyl bromide was administered to male and female F-344 rats orally, or by inhalation from a closed exposure system. DNA adducts were detected in the liver, lung, stomach and forestomach. [14C]3-Methyladenine, [14C]7-methylguanine and [14C]O6-methylguanine were identified using a combination of three different methods of hydrolysing DNA, followed by HPLC or gas chromatography-mass spectrometry. After both oral and inhalation exposure, the highest levels of methylated guanines, especially those of [14C]O6-methylguanine, were found in the stomach and forestomach of the rats. These results clearly demonstrate a systemic DNA-alkylating potential of methyl bromide.

A procedure for the extraction and high resolution two-dimensional gel electrophoresis of total nuclear phosphoproteins from isotonically purified nuclei

Methods are described for the extraction and preparation of total nuclear proteins for high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The conditions for protein extraction and preparation limit both protease and phosphatase activity, allowing application of this technique to the reliable analysis of changes in nuclear protein composition and nuclear protein phosphorylation as well as other forms of post-translational modifications. Unlike other procedures for 2-D PAGE analysis of nuclear proteins the technique allows solubilization and extraction of all nuclear proteins along with removal of nucleic acids which interfere with isoelectric focusing and autoradiography of 32Pi-labeled proteins. It avoids lengthy dialysis in which precipitation of nuclear proteins often occurs and does not require precipitation and resolubilization of nuclear proteins to obtain sufficient protein concentrations for 2-D PAGE analysis; often impractical steps in which complete resolubilization of all proteins is not possible. It produces high resolution 2-D PAGE analysis in which identification of even low abundance proteins can be made, based on isoelectric point and molecular weight, allowing comparison with other studies.

Pyruvate kinase inhibited by L-cysteine as a marker of tumorigenic human urothelial cell lines

It was found that a decrease in electrophoretic mobility of pyruvate kinase (PK) isoenzyme, and an increase of the sensitivity of this enzyme to L-cysteine, were markers of immortalization and tumorigenic properties, respectively, in human urothelial cell lines characterized by different grades of transformation (TGr) in vitro.

Localization, in human placenta, of the tightly bound form of DNA methylase in the higher order of chromatin organization

In human placenta, the DNA of all subfractions of the third level of chromatin organization exhibits similar values of the methylcytosine-to-cytosine ratio. The tightly bound form of DNA methyltransferase is mostly recovered in the 'stripped loop' fraction, although, on the basis of the DNA content, the 'stripped loops' and the 'stripped matrix' appear to possess a similar amount of the enzyme. DNA methyltransferase activity is instead totally absent from the 'digested matrix', i.e., from the fraction remaining after digestion of the 'stripped matrix' with DNAase I. Upon addition of exogenous DNA methyltransferase, however, the DNA of this fraction, which is only 1% (in weight) of the total chromatin DNA and which has a length of approx. 9 kbp, can readily undergo methylation.

Pyruvate kinase isoenzymes in chromatin extracts of Ehrlich ascites tumour, Morris hepatoma 7777 and normal mouse and rat livers

A pyruvate kinase (EC 2.7.1.40) variant inhibited by L-cysteine has been found in Ehrlich ascites tumour and Morris hepatoma 7777, but not in normal mouse and rat livers used for comparison. Chromatin extracts of all materials studied contained three pyruvate kinase isoenzymes (alpha, beta, gamma) which showed the greatest electrophoretic mobility in normal mouse and rat livers. The isoenzyme mobility diminished in both tumour chromatin extracts, and the slow migrating gamma isoenzyme exhibited sensitivity to L-cysteine inhibition. This gamma isoenzyme sensitive to L-cysteine might be considered as a tumour marker. All tumour pyruvate kinase isoenzymes were insensitive to normal signal molecules, i.e., to ATP and fructose 1,6-diphosphate, which regulate liver pyruvate kinase activity. It was, however, noted that the binding of pyruvate kinase isoenzymes to DNA is connected with a diminution in their catalytic activity.

Intranuclear distribution of rat liver glucocorticoid receptors by nuclease digestion in a cell-free system

Intranuclear distribution of rat liver glucocorticoid receptors was examined. When the [3H]TA-receptor complex-bound nuclei were digested with micrococcal nuclease, the [3H]TA-receptor complex sedimented coincident with mono-, di- and trinucleosomes on a glycerol gradient. The specific activity of the [3H]TA-receptor associated with chromatin fragments in the Mg-soluble fraction was 13-fold higher than that in the Mg-insoluble fraction. In adrenalectomized rats, the nucleosome-bound [3H]TA-receptor complex was reduced, but the specific activity in the Mg-soluble fraction was almost the same as that in intact rats. Endogenous glucocorticoid receptor complex associated with mononucleosomes decreased 2 weeks after adrenalectomy. These results suggest that interaction between the glucocorticoid receptor complex and chromatin acceptor sites in intact and adrenalectomized rats occurred in the transcriptionally active chromatin regions which are sensitive to micrococcal nuclease.

Tightly-bound non-histone proteins in different nucleosome-like subpopulations from pig kidney chromatin

By differential sucrose gradient centrifugation of pig kidney chromatin in the presence or absence of Na-EDTA and under varying ionic strength conditions, three nucleosome-like subpopulations with different buoyant densities can be obtained. These particles, on the basis of their histones and HMG protein pattern, of the 5-methylcytosine level of their DNA and of the RNA polymerase activity associated with them, can be considered as originating from chromatin fractions differently involved in gene expression. Two-dimensional electrophoresis of the tightly-bound non-histone proteins shows a distinct pattern for each subpopulation, such protein components being notably present in restricted numbers but in high amounts in the subpopulation which was apparently derived from condensed heterochromatin.

Characterization of the antigen reactive with anti-Scl-70 antibodies and its application in an enzyme-linked immunosorbent assay

The characteristics of the Scl-70 antigen (topoisomerase I) have been analyzed by means of autoantibodies. This antigen is a DNA-binding protein, dissociable from DNA at 0.3M NaCl and bound to a fraction of DNA that is very sensitive to nucleases. The molecular weight of the antigen is 105,000 daltons, whether dissociation conditions are used or not. Using chicken erythrocytes, and taking advantage of the strong interaction of the antigen with hydroxyapatite, we have designed a simple and fast purification protocol that allows the determination of anti-topoisomerase I antibodies by enzyme-linked immunosorbent assay.

Autoantibodies against the H1(0) subtype of histone H1

The specificity of antinuclear autoantibodies in a patient with a sensory neuropathy associated with cancer has been analyzed. The autoantibodies recognize the histone H1(0) as shown by its dissociation from DNA, perchloric solubility, electrophoretic mobility in SDS or urea/acid polyacrylamide gels, and by the capacity of purified H1(0) to block the reactivity of these autoantibodies. Almost no reactivity was observed with other subtypes of H1. To our knowledge, this is the first autoantibody described with such specific reactivity for the H1(0) subtype.

5-Methylcytosine levels in nucleosome subpopulations differently involved in gene expression

Sucrose density gradient centrifugation in the presence or absence of Na-EDTA and at different ionic strengths allows one to obtain well-defined nucleosome subpopulations the DNA of which, examined by gas chromatography-mass spectrometry, is in all cases hypermethylated as compared to spacer regions, but to a different extent for the different subpopulations. The various nucleosomes differ also in their content of histones and of high-mobility-group proteins, as well as in the levels of RNA polymerase activity associated with them. Such data suggest that these nucleosome subpopulations originate from chromatin fractions differently involved in gene expression.

A note on the use of protease inhibitors during chromatin fractionation on hydroxyapatite columns

It was found that NaHSO3 present in the eluents enabled full and reproducible recovery of chromosomal proteins from a hydroxyapatite column. Another protease inhibitor, PMSF, did not have that effect.

Thiol proteins in chromatin

Total half-cystine residues in proteins of pig liver chromatin have been measured. About half of them are present in the reduced state. Thiol groups of non-histone chromatin proteins, which amount to about 40 nmol/mg of protein, are preferentially located in chromatin fragments which are more easily solubilised either by DNAse I or by DNAse II. The data obtained are compatible with an involvement of SH and SS groups in chromatin structure and function.

Alkylation of nuclear proteins and DNA after exposure of rats and mice to [1,4-14C]1,3-butadiene

B6C3F1 mice and Wistar rats were exposed to [1,4-14C]1,3-butadiene in a closed exposure system. Based on body weight, mice metabolized the test compound at about twice the rate, compared to rats. Nucleoproteins and DNA were isolated from the livers of the animals and covalent binding of [14C]-butadiene-derived radioactivity was determined. In both species comparable amounts of radioactivity were covalently bound to liver DNA. Covalent binding to mouse-liver nucleoproteins was twice as high as in rats and thus it paralleled the higher metabolic rate for butadiene in this species.

Vinyl acetate: DNA-binding assay in vivo

The question of carcinogenicity of vinyl acetate led us to perform a DNA binding assay in vivo in rats, using 14C-labelled vinyl acetate. After administration of [14C]vinyl acetate to male and female Fischer-344 rats, either orally or by inhalation, no specific hepatic DNA adducts, known to occur after administration of labelled vinyl halides or vinyl carbamates, could be detected in hepatic tissues.

Age-dependent changes in the level of a 34 kDa DNA-binding protein in developing chick embryo liver

The relative amounts of a DNA-binding protein of 34 kDa increased during the early stages of development of chick embryo liver. The content of this protein reached a maximum in 18-19-day-old embryonic livers and decreased afterwards in older embryonic and post-natal chick livers. The 34 kDa polypeptide is the major DNA-binding protein (DBP) of embryonic liver and it preferentially binds to single-stranded DNA. The quantity of the 34 kDa DBP was relatively very low in embryonic muscle, heart and brain.

Distribution of tightly bound non-histone proteins in chromatin fractions obtained by DNAase II digestion

Digestion of pig liver chromatin with DNAse II afforded three different fractions which were characterized in terms of their DNA, RNA and tightly bound non-histone protein content, their DNA fragment size and their template activity. Two of these fractions are soluble after digestion with DNAase II and have been separated on the basis of their different solubility in MgCl2. A third fraction is not solubilized even after extensive digestion, although the size of its DNA is comparable to that of the enzyme solubilized fractions. The three fractions show qualitatively and quantitatively different distribution of tightly bound non-histone proteins, with specific protein components in each fraction; furthermore the non-solubilized fraction is greatly enriched in proteins tightly bound to DNA. From all the data obtained it can be suggested that the tightly bound proteins of the insoluble fraction may play, directly or indirectly, a role in maintaining an organized chromatin structure.

DNA-binding assay of methyl chloride

Fischer-344 rats and B6C3F1 mice of both sexes were exposed in closed chambers to 14C-labeled methyl chloride. Different clearance values from the gas phase of the system indicated that, based on body weight, mice metabolized the test compound much faster than rats. After isolation of DNA and nucleoproteins from liver and kidneys radioactivity was found in all macromolecular samples; this was ascribed to metabolic C1-incorporation. Radioactivity incorporation was particularly high in DNA of mouse kidneys, suggesting a high turnover to active C1 bodies (formaldehyde, formate) in this tissue. Analyses of DNA samples from kidneys of female and male mice showed neither 7-N-methylguanine nor O6-methylguanine. Hence, the formation of tumors in B6C3F1 mice exposed to high concentrations of methyl chloride is not based on methylation of DNA in this tissue.

Nucleosome disruption precedes transcription and is largely limited to the transcribed domain of globin genes in murine erythroleukemia cells

We used micrococcal nuclease to separate murine erythroleukemia cell (MELC) chromatin into soluble and insoluble fractions which differ in gene content and chromatin structure. Genes that are not expressed in the erythroid lineage, such as the Ig alpha and albumin genes, distribute preferentially into the soluble rather than the insoluble fraction, and are organized into nucleosomes in both fractions. Both alpha 1- and beta maj-globin genes are enriched in the insoluble fraction and are organized into structures that are partially devoid of nucleosomes in uninduced MELC, when the genes are transcriptionally inactive. Following chemical induction of MELC and the onset of globin gene transcription, globin gene enrichment and nucleosome disruption in the insoluble chromatin fraction increase. Using seven DNA subclones that span the beta maj-globin gene we show that insolubility and nucleosome disruption are largely limited to DNA sequences lying within the transcribed domain. Non-transcribed, flanking sequences are soluble and organized into nucleosomes. In addition, the globin genes found in insoluble, non-nucleosomal chromatin contain previously engaged RNA polymerases which can elongate globin RNA chains in vitro in a pattern qualitatively and quantitatively similar to intact nuclei. These results are discussed in terms of a model for globin gene activation during erythropoeisis.

Hepatoma-associated nonhistone chromosomal proteins

In order to compare nonhistone proteins in normal and neoplastic hepatocytes, we elicited antisera to Morris hepatoma 7777 dehistonized chromatin. By the enzyme-linked immunosorbent assay, the antisera demonstrated specificity for Morris hepatoma 7777 and little reactivity to normal rat liver chromatin. Morris hepatomas 7288c, 7800 and 5123tc shared some antigenic hepatoma nonhistone proteins. Neoplasia induced in rats fed 3'-methyl-4-dimethylaminoazobenzene changed the immunospecificity of the liver chromatin to a new type that was antigenically similar to Morris hepatoma 7777. Fetal rat liver chromatin and regenerating rat liver chromatin did not bind antibody. To further characterize the antigenic nonhistone proteins, we analyzed Morris hepatoma 7777 chromatin and normal rat liver chromatin by the immunoblot technique. Nonhistone proteins that demonstrated immunoreactivity were predominantly high molecular weight proteins.

Yeast centromere DNA is in a unique and highly ordered structure in chromosomes and small circular minichromosomes

We have examined the chromatin structure of the centromere regions of chromosomes III and XI in yeast by using cloned functional centromere DNAs (CEN3 and CEN11) as labeled probes. When chromatin from isolated nuclei is digested with micrococcal nuclease and the resulting DNA fragments separated electrophoretically and blotted to nitrocellulose filters, the centromeric nucleosomal subunits are resolved into significantly more distinct ladders than are those from the bulk of the chromatin. A discrete protected region of 220-250 bp of CEN sequence flanked by highly nuclease-sensitive sites was revealed by mapping the exact nuclease cleavage sites within the centromeric chromatin. On both sides of this protected region, highly phased and specific nuclease cutting sites exist at nucleosomal intervals (160 bp) for a total length of 12-15 nucleosomal subunits. The central protected region in the chromatin of both centromeres spans the 130 bp segment that exhibits the highest degree of sequence homology (71%) between functional CEN3 and CEN11 DNAs. This unique chromatin structure is maintained on CEN sequences introduced into yeast on autonomously replicating plasmids, but is not propagated through foreign DNA sequences flanking the inserted yeast DNA.

A non-steroidal gametic factor linked to DNA modulates delta-aminolevulinic acid synthase inducibility acting on liver transcriptional and translational processes

The effect of an acidic factor of low molecular weight (about 1,000 daltons), extracted from bovine spermatozoan DNA, on the inducibility of delta-aminolevulinic acid synthase by ethanol during aging in rat has been examined. The increased enzyme inducibility in 600-day old rats is supported by stimulation of transcriptional and translational processes; on the contrary, in 30-day old rats, the higher enzyme values induced by ethanol are significantly decreased after factor treatment. The active factor is strongly DNA-bound in the native spermatozoan DNA. This would imply a possible role in regulating gene expression in vivo.

Tightly bound non-histone proteins in nucleosomes from pig-liver chromatin

Core particles prepared by micrococcal nuclease digestion of pig liver chromatin have been adsorbed on hydroxyapatite and dissociated by gradual increase in ionic strength and finally by urea and guanidine. By this method non-histone proteins have been found to be associated with the core particles. Proteins tightly bound to the core particle DNA (i.e. dissociated only by urea and guanidine) have also been found: these are proteins with a limited heterogeneity, with respect to their molecular weights, since only six components are present with molecular weights ranging from 71000 to 20000. They show, furthermore, a peculiar amino acid composition. Other tightly bound proteins have been shown to be present only in the spacer regions. The existence of two different classes of tightly bound proteins probably reflects different modes of binding to the DNA, which are compatible or incompatible, respectively, with the simultaneous binding of the histone octamer.

Monoclonal antibodies against chromosomal proteins of Drosophila melanogaster: establishment of antibody producing cell lines and partial characterization of corresponding antigens

Total nuclear protein from the embryonic D. melanogaster cell line Kc and crude hydroxyapatite fractions thereof were used for immunization of mice. From the spleen cells of these mice we established 755 permanent lymphoid cell lines using the hybridoma technique originally developed by Köhler and Milstein (1975). Radioimmunoassay showed 455 of these cell lines secreted antibodies which bound to component(s) contained in the antigen mixtures used for immunization. Screening of 311 cell lines using indirect immunofluorescence revealed 58 lines whose antibodies showed a highly selective staining pattern on polytene chromosomes from the salivary glands of D. melanogaster third instar larvae. Eight of these cell lines were cloned and further characterized. We were able to order the staining patterns into three distinct classes based on the staining behaviour of the monoclonal antibodies: staining of active regions, staining of phase dark bands or staining of most interbands. The molecular weight of those antigens against which the monoclonal antibodies were directed was determined in SDS polyacrylamide gels.

Characterization of a non-histone chromosomal protein which stimulates RNA polymerase II

A non-histone chromosomal protein was extracted and purified 177-fold from rat liver nuclei which stimulated RNA synthesis in vitro catalyzed by wheat germ RNA polymerase II with either liver chromatin, or native or denaturated calf thymus DNA as template. The stimulatory non-histone chromosomal protein fraction was characterized as having a molecular weight of 66 000 and a pI = 8.2--9.0. No activity was found with Escherichia coli RNA polymerase and liver chromatin. The binding of the stimulatory non-histone chromosomal protein occurred exclusively with the chromatin template and not with RNA polymerase II as assessed by its interference with actinomycin D but not with alpha-amanitin, respectively.