A simple solubilization method for loosely and tightly chromatin-bound RNA polymerase II from rat liver nuclei

Rat liver chromatin-bound RNA polymerase II could be differentially solubilized into two distinct populations, loosely and tightly bound enzymes, by a simple method. By this method the recovery of the solubilized enzyme from the chromatin fraction could be increased considerably as compared with the procedure of Yu (1). The two chromatin-bound enzymes had different properties:

1. Loosely bound enzyme was easily extractable from chromatin with relatively mild ionic condition (0.5 M NaCl); the tightly bound enzyme had to be solubilized by more drastic conditions such as sonication or nuclease treatment.
2. Loosely bound enzyme could not efficiently transcribe the chromatin template, but the tightly bound enzyme was active toward the same template. The latter enzyme is involved in the tight complex with the RNA synthesis activating factors.
3. Cycloheximide treatment in vivo suggests that the two enzymes have different turn-over rates.

Therefore, with this simple solubilization method the functionally different two chromatin-bound RNA polymerase II activities can be estimated.     

Specificity of the histone lysine methyltransferases from rat brain chromatin

The histone lysine methyltransferases catalyze the transfer of methyl groups from S-adenosylmethionine to specific epsilon-N-lysine residues in the N-terminal regions of histones H3 and H4. These enzymes are located exclusively within the nucleus and are firmly bound to chromatin. The chromosomal bound enzymes do not methylate free or nonspecifically associated histones, while histones H3 and H4 within newly synthesized chromatin are methylated. These enzymes can be solubilized by limited digestion (10-16%) of chromosomal DNA from rapidly proliferating rat brain chromatin with micrococcal nuclease. Histone H3 lysine methyltransferase remained associated with a short DNA fragment throughout purification. Dissociation of the enzyme from the DNA fragment with DNAase digestion resulted in complete loss of enzyme activity; however, when this enzyme remained associated with DNA it was quite stable. Activity of the dissociated enzyme could not be restored upon the addition of sheared calf thymus or Escherichia coli DNA. Histone H3 lysine methyltransferase was found to methylate lysine residues in chromosomal bound or soluble histone H3, while H3 associated with mature nucleosomes was not methylated. The histone H4 lysine methyltransferase which was detectable in the crude nuclease digest was extremely labile, losing all activity upon further purification. We isolated a methyltransferase by DEAE-cellulose chromatography, which would transfer methyl groups to arginine residues in soluble histone H4. However, this enzyme would not methylate nucleosomal or chromosomal bound histone H4, nor were methylated arginine nucleosomal or chromosomal bound histone H4, nor were methylated arginine residues detectable upon incubating intact nuclei or chromatin with S-adenosylmethionine.     

Studies on the glycoprotein component of (Na+ +K+)-ATPase from dog fish salt gland. Binding to concanavalin A and removal of sialic acid by neuraminidase.

1. The presence of concanavalin A binding sugars in the glycoprotein component of a partially purified (Na++K+) ATPase preparation from dog fish salt gland was demonstrated by binding of a Triton X-100 extract of the enzyme and isolated glycoprotein to concanavalin A-Sepharose, and by binding of membrane-associated enzyme to free concanavalin A. 2. The binding of concanavalin A to the glycoprotein in both membrane-associated enzyme and a Lubrol extract of the enzyme had no effect on (Na++K+)-ATPase activity. Binding was completely inhibited by methyl-alpha-mannoside. Also, enzyme activity was not affected by removal of 50% of glycoprotein sialic acid by neuraminidase. These results suggest that the carbohydrate moiety of the glycoprotein does not play a catalytic role in the (Na++K+)-ATPase. 3. When a Triton X-100 extract of (Na++K+)-ATPase was chromatographed on concanavalin A-Sepharose, 37% of total protein was bound to the column and eluted by methyl-alpha-mannoside. The bound fraction was free of lipid, and contained not only the glycoprotein but also the large protein which is the catalytic subunit of the enzyme, and small amounts of other membrane derived proteins. The ratio of large protein to glycoprotein, as measured by the relative Coomassie blue absorbance of the two proteins separated by gel electrophoresis, was the same in the bound fraction as in the membrane. These results suggest that the glycoprotein and lareg protein are either associated together in the membrane or become associated during lipid replacement by Triton.     

Poly(A) polymerases of rat liver nuclei. Purification and specificity.

Two poly(A) polymerases were isolated from rat liver nuclei and purified more than one thousand times by ion exchange chromatography on DEAE-Sephadex and phosphocellulose columns as well as affinity chromatography on a chromosomal RNA-Sepharose column. One of the two enzymes is bound to chromatin and uses as primer chromosomal RNA, while the second one is localized in the nucleoplasm and uses as primer poly(A) and hnRNA isolated from chromatin. The two enzymes seem to participate in the polyadenylation of chromosomal RNA in vitro, by a coupled mechanism. According to this mechanism, the chromatin bound enzyme adds 120-130 adenosine nucleotides to chromosomal RNA and consequently the nucleoplasmic enzyme completes the poly-adenylation by adding 80-90 more AMP units to the polyadenylated end of chromosomal RNA.     

Upon the observation of superbeads in chromatin.

There exist some indications that nucleases recognize "superbeads" in chromatin. We show that a chromatin extract of rat liver which contains so-called "superbead"-peaks can be separated in a Mg++ soluble and a Mg++ insoluble fraction. The Mg++ insoluble fraction contains the full complement of histones and the expected DNA fragments, but has lost the characteristic peaks in sucrosegradient profiles. These discrete peaks are found in the Mg2+ soluble fraction of the chromatin extract. We give evidence that these peaks are RNP particles on the basis of their protein- and nucleic acid contents.     

The nonhistone chromosomal protein, H2A-specific protease, is selectively associated with nucleosomes containing histone H1

We have determined the distribution of the nucleosomal bound nonhistone chromosomal protein, H2A-specific protease, in calf thymus and liver chromatin. The protease was unevenly distributed in chromatin with domains containing histone H1 being selectively complexed with the enzyme. Moreover, the protease had a preference for the less compact chromatin domains enriched in the H1 subtypes H1a and -c. We have demonstrated that ubiquitinated H2A is a substrate of the H2A-specific protease and that the enzyme is a serine protease which can be inactivated with protease inhibitors only after it is released from the nucleosome. Possible functions of the protease in modulating chromatin structure are discussed.     

DNA swivel enzyme activity in a nuclear membrane fraction.

DNA swivel (nicking-rejoining) enzyme activity has been studied in various cell fractions of a human lymphoid cell line. Swivel activity is found only in chromatin and in a nuclear membrane fraction containing DNA and possessing endogenous DNA synthesizing activity. Twenty percent of the total swivel activity and less than one percent of the total DNA are in the membrane fraction. The swivel enzyme is more tightly bound to the membrane fraction than to the chromatin fraction. These observations suggest that the swivel enzyme may be a replication factor, specifically bound to replicating DNA in the membrane fraction.     

Effect of divalent metal ions on collagenase from Clostridium histolyticum.

The collagenase from Clostridium histolyticum (EC 3.4.24.3) degrades type IV collagen with Km 32 nM, indicating a high affinity for this substrate. Ferrous and ferric ions can inhibit Clostridium collagenase. Inhibition by Fe++ was of the mixed, non-competitive type, with Ki 90 microM. The inhibitory effect of Fe++ may be due to Zn++ displacement from the intrinsic functional center of this metalloprotease, since in the presence of excess amounts of Zn++ enzyme activity is retained. This inhibitory effect of Fe++ may be common for all types of collagenases, since this ion can also inhibit type IV collagenase purified from Walker 256 carcinoma, with IC50 80 microM. Cu++ can only partially inhibit Clostridium collagenase, while other divalent metal ions such as Cd++, Co++, Hg++, Mg++, Ni++ or Zn++ are devoid of any inhibitory effect on the enzyme.     

Chromatin organization in isolated nuclei: flow cytometric characterization employing forward and perpendicular light scatter

Flow cytometric perpendicular and forward light scatters have been employed to evaluate whether the changes in chromatin organization due to ionic strength, Mg++ concentration and pH, visible in electron microscopy, can be monitored by flow cytometry. The average intensity of the perpendicular light scatter signal increased as nuclear chromatin became decondensed by lowering the ionic strength or releasing H1 histone at low pH values. These results indicate that flow cytometry signals and in particular the perpendicular light scatter allow the detection of the conformational transitions in chromatin and may therefore be useful for studying cell cycle associated morphological changes in isolated nuclei.     

Proof of guanylate cyclase activity in the coronary artery of cattle]

Guanylate cyclase activities were identified in a soluble fraction and a particular fraction obtained from the Arteria coronaria of cattle. The Km-value was 1.0 +/- 0.7 - 10(-4) M for the enzyme substrate complex of the guanylate cyclase of the soluble fraction and 9.2 +/- 1.5 - 10(-4) M for the particular fraction. For the enzyme activity of the soluble fraction Mn++ cannot be replaced by Ca++ or Mg++, whereas for the enzyme activity of the particulate fraction Mn++ can be replaced by Mg++ but not by Ca++. The guanylate cyclase of the particulate fraction can be activated by acetylcholine. This activation can be cancelled by atropine. Acetylcholine exerts no influence on the guanylate cyclase activity of the soluble fraction. ATP inhibits the enzyme activities of both fractions whereas cAMP shows no influence on the guanylate cyclase activity.     

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.     

Differential conjugation of polyamines to calf nuclear and nucleolar proteins

Nuclei and nucleoli isolated from calf liver contain acid-precipitable putrescine, spermidine and spermine conjugates. The polyamines are released upon peptide bond hydrolysis. All of the nuclear putrescine conjugate and a major portion of the polyamine conjugates are localized within the nucleolus. Nuclei and nucleoli also contain, in proportions consistent with the nucleolar/nuclear protein ratio, the putative conjugating enzyme, transglutaminase, as well as amine acceptor substrates to which radiolabeled putrescine can be conjugated by endogenous enzyme. Extraction of the isolated organelles with saline solutions of increasing ionic strength showed a differential distribution of the polyamine derivatives: all the covalently linked putrescine was associated with the less soluble components of the chromatin residue, while the spermidine and spermine conjugates were associated with several salt-extractable protein fractions as well as tightly bound to the chromatin pellet. Mono-gamma-glutamyl putrescine was detected after proteolytic digestion of the 600 mM NaCl fraction, further suggesting the enzymatic action of transglutaminase(s) in the conjugation process.     

Selective excision of the centromere chromatin complex from Saccharomyces cerevisiae

We have taken advantage of the known structural parameters associated with centromere DNA in vivo to construct a CEN fragment that can be selectively excised from the chromatin DNA with restriction endonucleases. CEN3 DNA is organized in chromatin such that a 220-250-bp region encompassing the elements of centromere homology is resistant to nuclease digestion. Restriction enzyme linkers encoding the Bam HI-recognition site were ligated to a 289 base pair DNA segment that spans the 220-250-bp protected core (Bloom et al., 1984). Replacement of this CEN3-Bam HI linker cassette into a chromosome or plasmid results in formation of a complete structural and functional centromeric unit. A centromere core complex that retains its protected chromatin conformation can be selectively excised from intact nuclei by restriction with the enzyme Bam HI. The centromeric protein-DNA complex is therefore not dependent upon the intact torsional constrains on linear chromosomes for its structural integrity. Isolation of this complex provides a novel approach to characterizing authentic centromeric proteins bound to DNA in their native state.     

Norepinephrine induced alpha-adrenoceptor mediated increase in rat brain Na-K ATPase activity is dependent on calcium ion

It has been reported that norepinephrine increases Na-K ATPase activity by acting on -1 adrenoceptors. The mechanism of such an increase was investigated. The norepinephrine induced increase in synaptosomal Na-K ATPase activity was prevented by pretreating the rat brain homogenate with either EDTA, a divalent cation chelator or prazosin, an -1 adrenoceptor blocker. The norepinephrine and EGTA increased the Na-K ATPase activity in the synaptosome prepared from rat brain homogenate untreated with EDTA. The EGTA was ineffective in stimulating the enzyme activity if the synaptosome was prepared from homogenate treated with norepinephrine. However, the EGTA was effective in increasing the enzyme activity if the synaptosome was prepared from the homogenate treated with norepinephrine in the presence of prazosin.

Thus, norepinephrine did not increase the Na-K ATPase activity in the presence of EDTA or -1 adrenoceptor blocker. Similarly, the Ca⁺⁺ chelator, EGTA, could not increase the enzyme activity if the homogenate was pretreated with norepinephrine alone. However, if norpeinephrine action was blocked by -1 antagonist prazosin, EGTA increased the enzyme activity possibly by chelation of Ca⁺⁺. Further, chlorotetracycline fluorescence study showed that norepinephrine removes membrane bound Ca⁺⁺. Thus, it is likely that norepinephrine acts on adrenoceptors and removes membrane bound Ca⁺⁺ and thereby increases the Na-K ATPase activity in the synaptosome.     

Distribution along DNA of the bound carcinogen N-acetoxy-N-2-acetylaminofluorene in chromatin modified in vitro.

Chromatin from duck erythrocytes was modified in vitro by the carcinogen N-acetoxy-N-2-acetylaminofluorene (N-Ac-O-AAF). The distribution of the carcinogen along the DNA molecule was studied using staphylococcal nuclease which allows the fractionation of chromatin DNA into two zones. It was shown that the carcinogen binds preferentially to the regions of chromatin sensitive to the enzyme; however, the regions of DNA tightly bound to histones and resistant to the enzyme react comparatively well. The single-strand specific nuclease S1 which digests DNA modified by the carcinogen in vitro did not digest chromatin under the conditions used. Some possible mechanisms for the interaction of the carcinogen with chromatin are discussed.     

Terbium as a fluorescent probe for DNA and chromatin.

Terbium reacted with DNA and chromatin to form a complex in which terbium acted as a sensitive fluorescent probe. By measuring the narrow-line emission of Tb-3+ when DNA is selectively excited, the relative amount of Tb-3+ bound to the DNA can be calculated. Terbium was bound to DNA until one Tb-3+ was present for each phosphate group. After this point no more terbium was bound. TbCl3 was bound to chromatin in a linear manner until approximately 0.48 TbCl3 was added for each phosphate group in the chromatin-DNA solution. From these data it appears that 52% of the phosphate groups in chromatin were unavailable for binding. The binding of Tb-3+ to DNA can be reversed by prolonged dialysis against 0.5 M NaCl and chelating agents. The terbium ion is ideal in that it binds DNA tight enough so that completion of the reaction can be assumed but loose enough so that it can be removed by gentle means. Low concentrations of salt (up to 2 mM NaCl) enhance the quantum efficiency. Below pH 3 and above pH 7 the DNA-terbium complex will not form. Between pH 3 and pH 7 the quantum efficiency of the DNA terbium complex increases from either pH to a maximum at pH 5.5 to 5.6. Several biochemical uses for Tb-3+ ion are suggested.     

DNA topoisomerase I cleavage sites in DNA and in nucleoprotein complexes.

The intracellular substrate for eukaryotic DNA topoisomerases is chromatin rather than protein-free DNA. Yet, little is known about the action of topoisomerases on chromatin-associated DNA. We have analyzed to what extent the organization of DNA in chromatin influences the accessibility of DNA molecules for topoisomerase I cleavage in vitro. Using potassium dodecyl sulfate precipitation (Trask et al., 1984), we found that DNA in chromatin is cleaved by the enzyme with somewhat reduced efficiency compared to protein-free DNA. Furthermore, using native SV40 chromatin and mononucleosomes assembled in vitro, we show that DNA bound to histone octamer complexes is cleaved by topoisomerase I and that the cleavage sites as well as their overall distribution are identical in histone-bound and in protein-free DNA molecules.