The chemistry of the cell nucleus

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

Several recent studies have portrayed DNA methylation as a new player in the recruitment of transcription factors (TF) within chromatin, highlighting a need to connect TF binding sites (TFBS) with their respective DNA methylation profiles. However, current TFBS databases are restricted to DNA binding motif sequences. Here, we present MethMotif, a two-dimensional TFBS database that records TFBS position weight matrices along with cell type specific CpG methylation information computed from a combination of ChIP-seq and whole genome bisulfite sequencing datasets. Integrating TFBS motifs with TFBS DNA methylation better portrays the features of DNA loci recognised by TFs. In particular, we found that DNA methylation patterns within TFBS can be cell specific (e.g. MAFF). Furthermore, for a given TF, different DNA methylation profiles are associated with different DNA binding motifs (e.g. REST). To date, MethMotif database records over 500 TFBSs computed from over 2000 ChIP-seq datasets in 11 different cell types. MethMotif portal is accessible through an open source web interface (https://bioinfo-csi.nus.edu.sg/methmotif) that allows users to intuitively explore the entire dataset and perform both single, and batch queries.

Isolation of nuclei from yeast

A method for isolation of nuclei from Saccharomyces cervisiae in high yield is described. The DNA/protein ratio of the isolated nuclei is 10 times higher than that of whole cells. Examination of these nuclei in phase and electron microscopes has shown them to be round bodies having a double membrane, microtubules, and a dark crescent at one end. The optimum conditions for extraction and resolution of histones of these nuclei on acrylamide gels have been investigated. The nuclei have an active RNA polymerase (E.C. 2.7.7.6) and are able to synthesize RNA in vitro. They are also readily stainable with Giemsa's, Feulgen's, and acridine orange methods.

A general method for the specific staining of intracellular antigens with ferritin-antibody conjugates

A general method is described whereby an intracellular macromolecule can be specifically stained with its antibody conjugated to ferritin. In this method cells or cell organelles are fixed, embedded in bovine serum albumin cross-linked with glutaraldehyde or formaldehyde, and then sectioned. This procedure preserves antigenic determinants as well as the cellular ultrastructure. The application of the ferritin-antibody conjugate to the section produces specific staining of the exposed antigen.

A cytochemical study of the L. E. bodies of systemic lupus erythematosus. II. Proteins

Microspectrophotometric comparison of lymphocyte nuclei and free L.E. bodies which are derived from them show a more than twofold average increase in the latter of protein basic groups revealed by naphthol yellow S binding, and tyrosine residues demonstrated by the Millon reaction. The alkaline fast green method for histones and the Sakaguchi reaction for arginine residues suggest that there is a marked loss and ultimate disappearance of histones in the course of formation of the L.E. body from a nucleus. It is postulated that the L.E. transformation entails influx of protein normally foreign to the nucleus, displacement of histone from combination of DNA, and association of the DNA with the new protein which is then responsible for masking the anionic groups of DNA.

A cytochemical study of the L. E. bodies of systemic lupus erythematosus. I. Nucleic acids

The composition, with respect to nucleic acids, of the L.E. bodies resulting from the action of the plasma of patients with systemic lupus erythematosus on substrate leukocyte nuclei in different kinds of preparations was compared microspectrophotometrically with that of control lymphocyte nuclei. Binding of the basic dye methyl green to DNA was uniformly found to be depressed in L.E. bodies as compared with control nuclei. Since Feulgen-revealed DNA, which served as a standard of reference, was relatively unchanged in amount, the Feulgen:methyl green ratios of L.E. bodies were higher than those of lymphocyte nuclei. Acetylation, which covers basic groups of proteins, was found to increase methyl green uptake by DNA of L.E. bodies to values approximating those of control nuclei, with consequent revision, after acetylation of the Feulgen: methyl green ratios of L.E. bodies to values similar to those of lymphocyte nuclei. Ribonuclease was found to reduce methyl green staining; extraction with dilute acid had little effect. These data have been interpreted to indicate (a) the presence in L.E. bodies of DNA-associated proteins whose basic groups compete with the cationic dye for binding sites of DNA and so inhibit methyl green staining, and (b) the DNA itself is not detectibly altered in state or degree of polymerization. Photometric comparison of the mean Feulgen-stainable DNA content per L.E. body with that of control nuclei showed that DNA is not lost in the L.E. transformation of nuclei.

Experimentally induced chromosome aberrations in plants. I. The production of chromosome aberrations by cyanide and other heavy metal complexing agents

The finding of Lilly and Thoday that potassium cyanide produces structural chromosome changes in root tips of Vicia faba was confirmed. Like mustards, diepoxides, and maleic hydrazide, potassium cyanide seems to act on cells at early interphase. A tendency of cyanide breaks to be concentrated in heterochromatic segments of the chromosomes was evident. The production of chromosome aberrations by cyanide proved to be practically unaffected by the temperature during treatment. In agreement with Lilly and Thoday, the effect of potassium cyanide was found to be dependent on oxygen tension during treatment. The effect of potassium cyanide increases with increasing oxygen concentration up to 100 per cent oxygen. In the absence of oxygen, potassium cyanide was not completely inactive, but produced a low, though significant frequency of aberrations. Pretreatments with 2.4-dinitrophenol did not influence the effect of potassium cyanide. When bean roots were treated with potassium cyanide before a treatment with 8-ethoxycaffeine, or at the same time as they were treated with 8-ethoxycaffeine, the effect of 8-ethoxycaffeine was almost completely suppressed. The effects of a number of other heavy metal complexing agents were also tested. Sodium fluoride, potassium thiocyanate, carbon monoxide, o-phenanthroline, 2.2-bipyridine, and sodium azide were without radiomimetic effect under the conditions employed, and so was a mixture of sodium azide and sodium fluoride. A low, but quite significant, radiomimetic effect was obtained after treatments with sodium diethyldithiocarbamate, cupferron, and 8-hydroxyquinoline. Under anaerobic conditions, the effects of cyanide and cupferron were both quantitatively and qualitatively indistinguishable. Unlike the effect of cyanide, the effect of cupferron was not enhanced by the presence of oxygen. The effects of the same heavy metal complexing agents were tested on the activities of the enzymes catalase and peroxidase. The activities of both of these enzymes were found to be totally inhibited only by potassium cyanide. In the other cases, little correlation was found between ability to inhibit the activities of these enzymes and ability to produce chromosome aberrations. In a number of experiments, hydrogen peroxide was found to be without radiomimetic effect, whether alone or in combination with potassium cyanide. t-Butyl hydroperoxide proved to be active. The effect of t-butyl hydroperoxide was substantially increased by pretreatments with 2.4.-dinitrophenol. The results are discussed, and it is concluded that the observations made do not support the hypothesis that hydrogen peroxide is involved in the production of chromosome aberrations by potassium cyanide. The possibility that organic peroxides are involved cannot be excluded on the bases of the experimental results. As an alternative hypothesis, it is suggested that iron or other heavy metals are present in the chromosomes and that cyanide and other heavy metal complexing agents produce chromosome aberrations by reacting with these metals.

A study of chromosomes with the electron microscope

Amphibian lampbrush chromosomes and meiotic prophase chromosomes of various insects and plants consist of a bundle of microfibrils about 500 A thick. These fibrils are double, being made of two closely associated fibrils 200 A thick. Fragments of interphase nuclei contain a mass of fibrils 200 A thick. Ultrathin sections through nuclei in prophase or interphase show sections of these double or single fibrils cut at various angles. A comparison of sections with the methacrylate left in and sections that were shadowed after removing the methacrylate suggests that the OsO(4) reacts only with the outer part of the fibrils either because it does not penetrate, or as a result of a chemical difference of the inner core and the outside of the fibril. It is suggested that in analogy to the structure of the tobacco mosaic virus the chromosomal microfibril may have an inner core of DNA surrounded by a shell of protein.

The choice of the suspension medium for rat-liver-cell nuclei

Images